diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index bfb3b953c78ef124addc5b8a97a8c4f686591456..5b0af6c0d9a565936890112c99f0e0be982022b6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -248,6 +248,26 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") endif() endif() +####################################### +# add custom target for IWYU analysis +####################################### +set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") +mark_as_advanced(ENABLE_IWYU) +if(ENABLE_IWYU) + find_program(IWYU_EXE NAMES include-what-you-use iwyu) + find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) + if (IWYU_EXE AND IWYU_TOOL) + add_custom_target( + iwyu + ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp + COMMENT "Running IWYU") + add_dependencies(iwyu lammps) + else() + message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable" + "and the iwyu-tool/iwyu_tool script installed in your PATH") + endif() +endif() + set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)") mark_as_advanced(ENABLE_SANITIZER) set(ENABLE_SANITIZER_VALUES none address leak thread undefined) @@ -292,7 +312,6 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) endif() endif() - find_package(JPEG QUIET) option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND}) if(WITH_JPEG) diff --git a/cmake/iwyu/iwyu-extra-map.imp b/cmake/iwyu/iwyu-extra-map.imp new file mode 100644 index 0000000000000000000000000000000000000000..4fadea73fb3306bba6154eefd3d8aec0f86c7604 --- /dev/null +++ b/cmake/iwyu/iwyu-extra-map.imp @@ -0,0 +1,7 @@ +[ + { include: [ "", private, "", public ] }, + { include: [ "", public, "", public ] }, + { include: [ "@", private, "", public ] }, + { include: [ "@", private, "\"gtest/gtest.h\"", public ] }, + { include: [ "@", private, "\"gmock/gmock.h\"", public ] }, +] diff --git a/doc/include-file-conventions.md b/doc/include-file-conventions.md index e3448cb8ce05491c69a7e31c0a324cb3ba5b2d76..87b9eba8df44e9d130208a065d7eb131d03a0ed1 100644 --- a/doc/include-file-conventions.md +++ b/doc/include-file-conventions.md @@ -91,32 +91,31 @@ statements should follow the "include what you use" principle. Include files should be included in this order: * the header matching the implementation (`some_class.h` for file `some_class.cpp`) -* mpi.h -* system and library headers (anything that is using angular brackets; C-library headers first, then C++) +* mpi.h (only if needed) * LAMMPS local headers (preferably in alphabetical order) +* system and library headers (anything that is using angular brackets; preferably in alphabetical order) +* conditional include statements (i.e. anything bracketed with ifdefs) ### Special Cases and Exceptions #### pointers.h -The `pointer.h` header file also includes `cstdio`, `cstddef`, -`string`, `lmptype.h`, and `utils.h` (and through those indirectly - `stdint.h`, `intttypes.h`, cstdlib, and `climits`). +The `pointer.h` header file also includes (in this order) `lmptype.h`, +`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h` +and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`. This means any header including `pointers.h` can assume that `FILE`, -`NULL`, `INT_MAX` are defined, they may freely use std::string -and functions from the utils namespace without including the -corresponding header files. +`NULL`, `INT_MAX` are defined, and the may freely use the std::string +for arguments. Corresponding implementation files do not need to include +those headers. ## Tools The [Include What You Use tool](https://include-what-you-use.org/) can be used to provide supporting information about compliance with -the rules listed here. There are some limitations and the IWYU tool -may give incorrect advice. The tools is activated by setting the -CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the -path of the `include-what-you-use` command. When activated, the -tool will be run after each compilation and provide suggestions for -which include files should be added or removed. +the rules listed here. Through setting `-DENABLE_IWYU=on` when running +CMake, a custom build target is added that will enable recording +the compilation commands and then run the `iwyu_tool` using the +recorded compilation commands information when typing `make iwyu`. ## Legacy Code diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index baace2e063adfddf1d99dc8ef5ba0ea8208a0e6c..7548a8a6e96a0e9090c09716f01dafc37a2da5ea 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -115,12 +115,12 @@ self-installed MPICH or OpenMPI, so you should study the provided documentation to find out how to build and link with it. The majority of OpenMP (threading) support in LAMMPS is provided by the -``USER-OMP`` package; see the :doc:`Speed omp ` doc page for -details. The ``USER-INTEL`` package also includes OpenMP threading (it -is compatible with ``USER-OMP`` and will usually fall back on styles -from that package, if a ``USER-INTEL`` does not exist) and adds -vectorization support when compiled with compatible compilers, in -particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` +``USER-OMP`` package; see the :doc:`Speed_omp` +page for details. The ``USER-INTEL`` package also includes OpenMP +threading (it is compatible with ``USER-OMP`` and will usually fall +back on styles from that package, if a ``USER-INTEL`` does not exist) +and adds vectorization support when compiled with compatible compilers, +in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` package can be compiled to include OpenMP threading. In addition, there are a few commands in LAMMPS that have native OpenMP @@ -290,13 +290,13 @@ Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``): compiler that supports C++11; either as a binary package or through compiling from source. -If you build LAMMPS with any :doc:`accelerator packages -` included, there may be specific optimization flags +If you build LAMMPS with any :doc:`Speed_packages` included, there may +be specific compiler or linker flags that are either required or recommended to enable required features and to achieve optimal performance. You need to include these in the CCFLAGS and LINKFLAGS settings above. For details, see the individual -package doc pages listed on the :doc:`Speed packages ` -doc page. Or examine these files in the src/MAKE/OPTIONS directory. +package doc pages listed on the :doc:`Speed_packages` +page. Or examine these files in the src/MAKE/OPTIONS directory. They correspond to each of the 5 accelerator packages and their hardware variants: @@ -418,7 +418,7 @@ recommended to ensure the integrity of the system software installation. .. _debug: -Excluding or removing debug support +Including or removing debug support ----------------------------------- By default the compilation settings will include the *-g* flag which @@ -460,7 +460,7 @@ python packages are installed into that virtual environment via the pip tool. The actual translation is then done via make commands. .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html -.. _sphinx: https://sphinx-doc.org +.. _sphinx: https://www.sphinx-doc.org Documentation make option ^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/src/Build_development.rst b/doc/src/Build_development.rst index cd432dddcb86764386dc2ae018ebaa5e8ffd6f78..cf3e2fb750c86c3da9874f081213454204c788c1 100644 --- a/doc/src/Build_development.rst +++ b/doc/src/Build_development.rst @@ -28,6 +28,40 @@ variable VERBOSE set to 1: ---------- +.. _iwyu_processing: + +Report missing and unneeded '#include' statements +------------------------------------------------- + +The conventions for how and when to use and order include statements in +LAMMPS are `documented in a separate file `_ +(also included in the source code distribution). To assist with following +these conventions one can use the `Include What You Use tool `_. +This is still under development and for large and complex projects like LAMMPS +there are some false positives, so suggested changes need to be verified manually. +It is recommended to use at least version 0.14, which has much fewer incorrect +reports than earlier versions. + +The necessary steps to generate the report can be enabled via a +CMake variable: + +.. code-block:: bash + + -D ENABLE_IWYU=value # value = no (default) or yes + +This will check if the required binary (include-what-you-use or iwyu) +and python script script (iwyu-tool or iwyu_tool or iwyu_tool.py) can +be found in the path. The analysis can then be started with: + +.. code-block:: bash + + make iwyu + +This may first run some compilation, as the analysis is dependent +on recording all commands required to do the compilation. + +---------- + .. _sanitizer: Address, Undefined Behavior, and Thread Sanitizer Support @@ -37,14 +71,14 @@ Compilers such as GCC and Clang support generating instrumented binaries which use different sanitizer libraries to detect problems in the code during run-time. They can detect issues like: - - `memory leaks `_ + - `memory leaks `_ - `undefined behavior `_ - `data races `_ Please note that this kind of instrumentation usually comes with a performance hit (but much less than using tools like `Valgrind -`_ with a more low level approach). The to enable -these features additional compiler flags need to be added to the +`_ with a more low level approach). To enable +these features, additional compiler flags need to be added to the compilation and linking stages. This is done through setting the ``ENABLE_SANITIZER`` variable during configuration. Examples: @@ -77,7 +111,7 @@ error margin). The status of this automated testing can be viewed on The unit testing facility is integrated into the CMake build process of the LAMMPS source code distribution itself. It can be enabled by setting ``-D ENABLE_TESTING=on`` during the CMake configuration step. -It requires the `YAML `_ library and development +It requires the `PyYAML `_ library and development headers to compile and will download and compile a recent version of the `Googletest `_ C++ test framework for implementing the tests. diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index b72dd95046a4d3609b80d4376de37affe6357d51..9595849b583526226e5b690cf61ecddb84aab170 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -234,11 +234,10 @@ command, you also need to have libcurl installed with the matching development headers and the curl-config tool. If you would like to use the :doc:`kim_property ` -command, you need to build LAMMPS with the Python 3.6 or later package -installed. See the :doc:`Python ` doc page for more info on building -LAMMPS with the version of Python on your system. -After successfully building LAMMPS with Python, you need to -install the kim-property Python package, which can be easily done using +command, you need to build LAMMPS with the PYTHON package installed +and linked to Python 3.6 or later. See the :ref:`PYTHON package build info ` +for more details on this. After successfully building LAMMPS with Python, you +also need to install the kim-property Python package, which can be easily done using *pip* as ``pip install kim-property``, or from the *conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in Conda. More detailed information is available at: @@ -812,10 +811,11 @@ a corresponding ``Makefile.lammps.machine`` file. PYTHON package --------------------------- -Building with the PYTHON package requires you have a Python shared -library available on your system, which needs to be a Python 2.7 -version or a Python 3.x version. See ``lib/python/README`` for more -details. +Building with the PYTHON package requires you have a the Python development +headers and library available on your system, which needs to be a Python 2.7 +version or a Python 3.x version. Since support for Python 2.x has ended, +using Python 3.x is strongly recommended. See ``lib/python/README`` for +additional details. CMake build ^^^^^^^^^^^ @@ -1095,7 +1095,7 @@ USER-PLUMED package Before building LAMMPS with this package, you must first build PLUMED. PLUMED can be built as part of the LAMMPS build or installed separately -from LAMMPS using the generic `plumed installation instructions `_. +from LAMMPS using the generic `PLUMED installation instructions `_. The USER-PLUMED package has been tested to work with Plumed versions 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations with a different version of the Plumed kernel. @@ -1262,7 +1262,7 @@ To build with this package, you must choose which hardware you want to build for, either x86 CPUs or Intel KNLs in offload mode. You should also typically :ref:`install the USER-OMP package `, as it can be used in tandem with the USER-INTEL package to good effect, as explained -on the :doc:`Speed intel ` doc page. +on the :doc:`Speed_intel` page. When using Intel compilers version 16.0 or later is required. You can also use the GNU or Clang compilers and they will provide performance diff --git a/doc/src/Build_link.rst b/doc/src/Build_link.rst index 914142b3ceb16089cfbd618b96bcb80e087a8226..87899739bc97f0beddd891a0bed4da260f126ac4 100644 --- a/doc/src/Build_link.rst +++ b/doc/src/Build_link.rst @@ -4,11 +4,11 @@ Link LAMMPS as a library to another code LAMMPS is designed as a library of C++ objects that can be integrated into other applications including Python scripts. The files ``src/library.cpp`` and ``src/library.h`` define a -C-style API for using LAMMPS as a library. See the :doc:`Howto -library ` page for a description of the interface -and how to use it for your needs. +C-style API for using LAMMPS as a library. See the +:doc:`Howto_library` page +for a description of the interface and how to use it for your needs. -The :doc:`Build basics ` doc page explains how to build +The :doc:`Build_basics` page explains how to build LAMMPS as either a shared or static library. This results in a file in the compilation folder called ``liblammps.a`` or ``liblammps_.a`` in case of building a static library. In case of a shared library diff --git a/doc/src/Build_make.rst b/doc/src/Build_make.rst index af5e319121768b41b0016f9be88f83a31965dfb8..cd71fd46e6d5f002847170c7f4a83fd541dc68b7 100644 --- a/doc/src/Build_make.rst +++ b/doc/src/Build_make.rst @@ -37,7 +37,7 @@ enable (or "install") them first, as discussed on the :doc:`Build package ` doc page. If a packages requires (provided or external) libraries, you must configure and build those libraries **before** building LAMMPS itself and especially **before** enabling -such a package with ``make yes-``. Building :doc:`LAMMPS with +such a package with ``make yes-``. :doc:`Building LAMMPS with CMake ` can automate much of this for many types of machines, especially workstations, desktops, and laptops, so we suggest you try it first when building LAMMPS in those cases. diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst index 859bec988916130c786f9f26981a1b66c41f96de..21107b72037752cbbca5c35a9c27e4a421348d3d 100644 --- a/doc/src/Build_settings.rst +++ b/doc/src/Build_settings.rst @@ -6,7 +6,7 @@ explain how to do this for building both with CMake and make. * :ref:`C++11 standard compliance ` when building all of LAMMPS * :ref:`FFT library ` for use with the :doc:`kspace_style pppm ` command -* :ref:`Size of LAMMPS data types ` +* :ref:`Size of LAMMPS integer types ` * :ref:`Read or write compressed files ` * :ref:`Output of JPG and PNG files ` via the :doc:`dump image ` command * :ref:`Output of movie files ` via the :doc:`dump_movie ` command @@ -123,7 +123,8 @@ per-timestep CPU cost, FFTs are only a portion of long-range Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel communication can be costly). A breakdown of these timings is printed to the screen at the end of a run when using the -:doc:`kspace_style pppm ` command. The :doc:`Run output ` +:doc:`kspace_style pppm ` command. The +:doc:`Screen and logfile output ` doc page gives more details. A more detailed (and time consuming) report of the FFT performance is generated with the :doc:`kspace_modify fftbench yes ` command. diff --git a/doc/src/Build_windows.rst b/doc/src/Build_windows.rst index 4aacea9dfaafb47cd3652289ba2a7acbf5e51bf0..2df3fdd24ee0735f093b33acb91c637d0ac77746 100644 --- a/doc/src/Build_windows.rst +++ b/doc/src/Build_windows.rst @@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu from within Windows and from there on, you can pretty much use that shell like you are running on an Ubuntu Linux machine (e.g. installing software via apt-get and more). For more details on that, please -see :doc:`this tutorial ` +see :doc:`this tutorial `. .. _gnu: diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index e137e39a0868dc4b6b74c5dc36ce8acb1e22fc0e..1f6da5794564c2cc10005fae736fa1fcf51e1282 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -17,6 +17,11 @@ ways through the :doc:`compute chunk/atom ` command and then averaging is done using :doc:`fix ave/chunk `. Please refer to the :doc:`chunk HOWTO ` section for an overview. +Reset_ids command +----------------- + +The reset_ids command has been renamed to :doc:`reset_atom_ids `. + MEAM package ------------ @@ -27,7 +32,7 @@ which removes several restrictions (e.g. there can be multiple instances in hybrid pair styles) and allows for some optimizations leading to better performance. The new pair style :doc:`meam/c ` has the exact same syntax as the old "meam" pair style and thus pair style -:doc:`meam ` is an alias to the new style and backward +meam is an alias to the new style and backward compatibility of old inputs is preserved. REAX package diff --git a/doc/src/Errors_bugs.rst b/doc/src/Errors_bugs.rst index ff0b155795397efbaa0d0675c17e9a4ebb5a2821..d2714c86b18f7f49aeedde134e49f87961d9403c 100644 --- a/doc/src/Errors_bugs.rst +++ b/doc/src/Errors_bugs.rst @@ -6,23 +6,25 @@ the steps outlined below: * Check the `New features and bug fixes `_ section of the `LAMMPS WWW site - `_ to see if the bug has already been addressed in a patch. + `_ or the + `GitHub Releases page `_ to + see if the bug has already been addressed in a patch release. * Check that your issue can be reproduced with the latest development version of LAMMPS. * Check the manual carefully to verify that the unexpected behavior you are observing is indeed in conflict with the documentation - * Check the `GitHub Issue page `_ + * Check the `GitHub Issue page `_ if your issue has already been reported and if it is still open. - * Check the `GitHub Pull Requests page `_ - if there is already a fix for your bug pending. + * Check the `GitHub Pull Requests page `_ + to see if there is already a fix for your bug pending. * Check the `mailing list archives `_ to see if the issue has been discussed before. If none of these steps yields any useful information, please file a new -bug report on the `GitHub Issue page `_. The website will offer -you to select a suitable template with explanations and then you should -replace those explanations with the information that you can provide to -reproduce your issue. +bug report on the `GitHub Issue page `_. +The website will offer you to select a suitable template with explanations +and then you should replace those explanations with the information that +you can provide to reproduce your issue. The most useful thing you can do to help us verify and fix a bug is to isolate the problem. Run it on the smallest number of atoms and fewest @@ -33,7 +35,7 @@ Please avoid using binary restart files unless the issue requires it. In the latter case you should also include an input deck to quickly generate this restart from a data file or a simple additional input. This input deck can be used with tools like a debugger or `valgrind -`_ to further :doc:`debug the crash `. +`_ to further :doc:`debug the crash `. You may also send an email to the LAMMPS mailing list at "lammps-users at lists.sourceforge.net" describing the problem with the @@ -44,6 +46,3 @@ is overlooked and then forgotten. Issues on GitHub have to be explicitly closed, so that will *guarantee* that at least one LAMMPS developer will have looked at it. -.. _lws: https://lammps.sandia.gov -.. _gip: https://github.com/lammps/issues -.. _valgrind: https://valgrind.org diff --git a/doc/src/Errors_common.rst b/doc/src/Errors_common.rst index 34567db385d695e2ab1ffe5d15751ceeb030e43f..4d4483efecd38de9eb91a72d77a91557a115c2c0 100644 --- a/doc/src/Errors_common.rst +++ b/doc/src/Errors_common.rst @@ -48,8 +48,10 @@ to see it on the screen. If you get an error like "Invalid ... style", with ... being fix, compute, pair, etc, it means that you mistyped the style name or that the command is part of an optional package which was not compiled into your executable. The list of -available styles in your executable can be listed by using :doc:`the -h command-line swith `. The installation and -compilation of optional packages is explained on the :doc:`Build packages ` doc page. +available styles in your executable can be listed by using +:doc:`the -h command-line switch `. The installation and +compilation of optional packages is explained on the +:doc:`Build packages ` doc page. For a given command, LAMMPS expects certain arguments in a specified order. If you mess this up, LAMMPS will often flag the error, but it diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst index dc122f2c78ee5099520bdfe8387320cc68db030b..8a76dca66ea8f18fae87738cef026d706d5579bb 100644 --- a/doc/src/Examples.rst +++ b/doc/src/Examples.rst @@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the :doc:`dump image ` doc page. Animations of many of the examples can be viewed on the Movies section -of the `LAMMPS web site `_. +of the `LAMMPS web site `_. There are two kinds of sub-directories in the examples folder. Lower case named directories contain one or a few simple, quick-to-run @@ -223,4 +223,3 @@ instructions. See the :doc:`Packages_details ` doc page for more info on specific USER packages. .. _openkim: https://openkim.org -.. _lws: https://lammps.sandia.gov diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 89c0ce9ffef1b7d040793f88931f7ac70b3b3ba6..6d8f6e90548f18533a8fee3e15bf78a8c3dbde71 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -3,7 +3,7 @@ Howto discussions These doc pages describe how to perform various tasks with LAMMPS, both for users and developers. The -`glossary `_ website page also lists MD +`glossary `_ website page also lists MD terminology with links to corresponding LAMMPS manual pages. The example input scripts included in the examples directory of the LAMMPS distribution and highlighted on the :doc:`Examples ` doc page diff --git a/doc/src/Howto_2d.rst b/doc/src/Howto_2d.rst index 1b4be32106876eb53bb8d8e6579fa08e669862b4..9cf76ac3b092f01d4404e33817c486e72fe5310b 100644 --- a/doc/src/Howto_2d.rst +++ b/doc/src/Howto_2d.rst @@ -6,14 +6,14 @@ Use the :doc:`dimension ` command to specify a 2d simulation. Make the simulation box periodic in z via the :doc:`boundary ` command. This is the default. -If using the :doc:`create box ` command to define a +If using the :doc:`create_box ` command to define a simulation box, set the z dimensions narrow, but finite, so that the -create_atoms command will tile the 3d simulation box with a single z -plane of atoms - e.g. +:doc:`create_atoms ` command will fill the 3d simulation +box with a single z plane of atoms - e.g. .. code-block:: LAMMPS - :doc:`create box ` 1 -10 10 -10 10 -0.25 0.25 + create box 1 -10 10 -10 10 -0.25 0.25 If using the :doc:`read data ` command to read in a file of atom coordinates, set the "zlo zhi" values to be finite but narrow, diff --git a/doc/src/Howto_body.rst b/doc/src/Howto_body.rst index 36e40a88bdcdfe0173f84cd5e31f11c94d9e1d15..0c0a9302215dac08b145024c47fa60e18a757ec7 100644 --- a/doc/src/Howto_body.rst +++ b/doc/src/Howto_body.rst @@ -32,9 +32,9 @@ thus how they can be used to compute pairwise body/body or bond/non-body (point particle) interactions. More details of each style are described below. -More styles may be added in the future. See the :doc:`Modify body -` doc page for details on how to add a new body style to -the code. +More styles may be added in the future. See the +:doc:`page on creating new body styles ` for details on +how to add a new body style to the code. ---------- diff --git a/doc/src/Howto_chunk.rst b/doc/src/Howto_chunk.rst index 75fb30815b5585fd0b0dfc2b1d00d422cf35bf56..c0a7792448b03b46c8e83630e5a2e3997e19455e 100644 --- a/doc/src/Howto_chunk.rst +++ b/doc/src/Howto_chunk.rst @@ -198,7 +198,8 @@ explained on the :doc:`compute chunk/spread/atom ` co (7) An example for using one set of per-chunk values for molecule chunks, to create a second set of micelle-scale chunks (clustered -molecules, due to hydrophobicity), is explained on the :doc:`compute chunk/reduce ` command doc page. +molecules, due to hydrophobicity), is explained on the +:doc:`compute reduce/chunk ` command doc page. (8) An example for using one set of per-chunk values (dipole moment vectors) for molecule chunks, spreading the values to each atom in diff --git a/doc/src/Howto_drude.rst b/doc/src/Howto_drude.rst index 62659711c4c5179986956739fbd974b8c821dc0a..c866340e77522d981fa35cffe93dd91cba22bb21 100644 --- a/doc/src/Howto_drude.rst +++ b/doc/src/Howto_drude.rst @@ -29,7 +29,7 @@ molecular systems (:ref:`Lamoureux and Roux `): to the total charge of the core atom). A detailed tutorial covering the usage of Drude induced dipoles in -LAMMPS is on the :doc:`Howto drude2e ` doc page. +LAMMPS is on the :doc:`here `. As with the core-shell model, the cores and Drude particles should appear in the data file as standard atoms. The same holds for the diff --git a/doc/src/Howto_drude2.rst b/doc/src/Howto_drude2.rst index cbdbc2d250b37fa9eccbe053765828a926d3e94a..3dacf99decf34971c4f5ab1d2278bd9c7e2631be 100644 --- a/doc/src/Howto_drude2.rst +++ b/doc/src/Howto_drude2.rst @@ -377,7 +377,7 @@ For our phenol example, the groups would be defined as Note that with the fixes *drude/transform*\ , it is not required to specify *comm_modify vel yes* because the fixes do it anyway (several times and for the forces also). To avoid the flying ice cube artifact -:ref:`(Lamoureux) `, where the atoms progressively freeze and the +:ref:`(Lamoureux and Roux) `, where the atoms progressively freeze and the center of mass of the whole system drifts faster and faster, the *fix momentum* can be used. For instance: @@ -456,7 +456,7 @@ NPT ensemble using Nose-Hoover thermostat: .. _Lamoureux2: -**(Lamoureux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) +**(Lamoureux and Roux)** Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003) .. _Schroeder: diff --git a/doc/src/Howto_github.rst b/doc/src/Howto_github.rst index 795af96e0afeaed5bb7dcda79600eb0a24b2352d..63cb8945e8551c8671d8afac58778ec30b8253f7 100644 --- a/doc/src/Howto_github.rst +++ b/doc/src/Howto_github.rst @@ -20,7 +20,7 @@ work required by the LAMMPS developers. Consequently, creating a pull request will increase your chances to have your contribution included and will reduce the time until the integration is complete. For more information on the requirements to have your code included into LAMMPS -please see the :doc:`Modify contribute ` doc page. +please see :doc:`this page `. ---------- diff --git a/doc/src/Howto_spherical.rst b/doc/src/Howto_spherical.rst index 7ca8a1b0600e77042c3852c17d4da6e6d3bfe454..aa17e6ce21da9a4535de86cf34450ec22f8f2819 100644 --- a/doc/src/Howto_spherical.rst +++ b/doc/src/Howto_spherical.rst @@ -114,7 +114,7 @@ will only rotate and experience torque if the force field computes such interactions. These are the various :doc:`pair styles ` that generate torque: * :doc:`pair_style gran/history ` -* :doc:`pair_style gran/hertzian ` +* :doc:`pair_style gran/hertz ` * :doc:`pair_style gran/no_history ` * :doc:`pair_style dipole/cut ` * :doc:`pair_style gayberne ` diff --git a/doc/src/Howto_thermostat.rst b/doc/src/Howto_thermostat.rst index 77745efa57a06bfcb0522b132873ee7ea83fb176..7bddb1c89da9af7328c0b5c3fa2f917b91be5388 100644 --- a/doc/src/Howto_thermostat.rst +++ b/doc/src/Howto_thermostat.rst @@ -42,12 +42,12 @@ particles. DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of :doc:`fix langevin `. -Any of the thermostatting fixes can use :doc:`temperature computes ` that remove bias which has two -effects. First, the current calculated temperature, which is compared -to the requested target temperature, is calculated with the velocity -bias removed. Second, the thermostat adjusts only the thermal -temperature component of the particle's velocities, which are the -velocities with the bias removed. The removed bias is then added back +Any of the thermostatting fixes can be instructed to use custom temperature +computes that remove bias which has two effects: first, the current +calculated temperature, which is compared to the requested target temperature, +is calculated with the velocity bias removed; second, the thermostat adjusts +only the thermal temperature component of the particle's velocities, which are +the velocities with the bias removed. The removed bias is then added back to the adjusted velocities. See the doc pages for the individual fixes and for the :doc:`fix_modify ` command for instructions on how to assign a temperature compute to a @@ -55,7 +55,24 @@ thermostatting fix. For example, you can apply a thermostat to only the x and z components of velocity by using it in conjunction with :doc:`compute temp/partial `. Of you could thermostat only the thermal temperature of a streaming flow of -particles without affecting the streaming velocity, by using :doc:`compute temp/profile `. +particles without affecting the streaming velocity, by using +:doc:`compute temp/profile `. + +Below is a list of some custom temperature computes that can be used like that: + +* :doc:`compute_temp_asphere` +* :doc:`compute_temp_body` +* :doc:`compute_temp_chunk` +* :doc:`compute_temp_com` +* :doc:`compute_temp_deform` +* :doc:`compute_temp_partial` +* :doc:`compute_temp_profile` +* :doc:`compute_temp_ramp` +* :doc:`compute_temp_region` +* :doc:`compute_temp_rotate` +* :doc:`compute_temp_sphere` + + .. note:: diff --git a/doc/src/Howto_viscosity.rst b/doc/src/Howto_viscosity.rst index 8c7eb91b125244b3d551e7b3d0864a967b906484..cfe94976655a26272f947aafdaec771c7380534f 100644 --- a/doc/src/Howto_viscosity.rst +++ b/doc/src/Howto_viscosity.rst @@ -5,8 +5,8 @@ The shear viscosity eta of a fluid can be measured in at least 6 ways using various options in LAMMPS. See the examples/VISCOSITY directory for scripts that implement the 5 methods discussed here for a simple Lennard-Jones fluid model and 1 method for SPC/E water model. -Also, see the :doc:`Howto kappa ` doc page for an analogous discussion for -thermal conductivity. +Also, see the :doc:`page on calculating thermal conductivity ` +for an analogous discussion for thermal conductivity. Eta is a measure of the propensity of a fluid to transmit momentum in a direction perpendicular to the direction of velocity or momentum diff --git a/doc/src/Install_git.rst b/doc/src/Install_git.rst index 96a15323f43760ef419bff33ae4e9cb1b8a38f82..868f679dbc420b1c72fa52714907979436037bae 100644 --- a/doc/src/Install_git.rst +++ b/doc/src/Install_git.rst @@ -51,15 +51,14 @@ Or they can be generated from the content provided in doc/src by typing ``make html`` from the doc directory. After initial cloning, as bug fixes and new features are added to -LAMMPS, as listed on :doc:`this page `, you can stay -up-to-date by typing the following git commands from within the -"mylammps" directory: +LAMMPS you can stay up-to-date by typing the following git commands +from within the "mylammps" directory: .. code-block:: bash $ git checkout unstable # not needed if you always stay in this branch - $ git checkout stable # use one of the 3 checkout commands - $ git checkout master + $ git checkout stable # use one of these 3 checkout commands + $ git checkout master # to choose the branch to follow $ git pull Doing a "pull" will not change any files you have added to the LAMMPS @@ -82,8 +81,8 @@ Stable versions and what tagID to use for a particular stable version are discussed on `this page `_. Note that this command will print some warnings, because in order to get back to the latest revision and to be able to update with ``git pull`` -again, you first will need to first type ``git checkout unstable`` (or -check out any other desired branch). +again, you will need to do ``git checkout unstable`` (or +check out any other desired branch) first. Once you have updated your local files with a ``git pull`` (or ``git checkout``), you still need to re-build LAMMPS if any source files have @@ -95,7 +94,7 @@ changed. To do this, you should cd to the src directory and type: $ make package-update # sync package files with src files $ make foo # re-build for your machine (mpi, serial, etc) -just as described on the :doc:`Install patch ` doc page, +just as described on the :doc:`Apply patch ` doc page, after a patch has been installed. .. warning:: diff --git a/doc/src/Install_patch.rst b/doc/src/Install_patch.rst index 3acd72753f0e31a491d1e9b5be125af66cb2af1c..0bbd7bbf009425889653e3e44a2905773c1cdb2c 100644 --- a/doc/src/Install_patch.rst +++ b/doc/src/Install_patch.rst @@ -6,9 +6,12 @@ if you use git to track the LAMMPS development. Instructions for how to stay current are on the :doc:`Download the LAMMPS source with git ` page. -If you prefer to download a tarball, as described on the :doc:`Install git ` doc page, you can stay current by +If you prefer to download a tarball, as described on the +:doc:`tarball download ` page, you can stay current by downloading "patch files" when new patch releases are made. A link to -a patch file is posted on the `bug and feature page `_ of the LAMMPS website, along +a patch file is posted on the +`bugf fixes and new feature page `_ +of the LAMMPS website, along with a list of changed files and details about what is in the new patch release. This page explains how to apply the patch file to your local LAMMPS directory. diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index cff198da7049585dcc0d70b42ad60c5ee4e54773..acf27455cfe85c5f01557ca0a5ef0aa36bbd1ce3 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -181,7 +181,7 @@ Pre- and post-processing * A handful of pre- and post-processing tools are packaged with LAMMPS, some of which can convert input and output files to/from formats used - by other codes; see the :doc:`Toos ` doc page. + by other codes; see the :doc:`Tools ` doc page. * Our group has also written and released a separate toolkit called `Pizza.py `_ which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is @@ -197,7 +197,7 @@ Specialized features ---------------------------------- LAMMPS can be built with optional packages which implement a variety -of additional capabilities. See the :doc:`Packages ` doc +of additional capabilities. See the :doc:`Optional Packages ` page for details. These are LAMMPS capabilities which you may not think of as typical @@ -214,7 +214,7 @@ classical MD options: * Monte Carlo via :doc:`GCMC ` and :doc:`tfMC ` and :doc:`atom swapping ` * :doc:`path-integral molecular dynamics (PIMD) ` and :doc:`this as well ` * :doc:`Direct Simulation Monte Carlo ` for low-density fluids -* :doc:`Peridynamics mesoscale modeling ` +* :doc:`Peridynamics modeling ` * :doc:`Lattice Boltzmann fluid ` * :doc:`targeted ` and :doc:`steered ` molecular dynamics * :doc:`two-temperature electron model ` diff --git a/doc/src/Intro_nonfeatures.rst b/doc/src/Intro_nonfeatures.rst index fb41b9a054b8ca301f54360223d5ab930f3b6599..a22a726bdcf164135834b0e4f9b881a29be8f3ac 100644 --- a/doc/src/Intro_nonfeatures.rst +++ b/doc/src/Intro_nonfeatures.rst @@ -66,8 +66,10 @@ Here are suggestions on how to perform these tasks: on-the-fly via its :doc:`dump image ` command and pass them to an external program, `FFmpeg `_ to generate movies from them. For high-quality, interactive visualization there are - many excellent and free tools available. See the `Other Codes page `_ page of the LAMMPS website for - visualization packages that can use LAMMPS output data. + many excellent and free tools available. See the + `Visualization Tools `_ page of the + LAMMPS website for + visualization packages that can process LAMMPS output data. * **Plotting:** See the next bullet about Pizza.py as well as the :doc:`Python ` doc page for examples of plotting LAMMPS output. Scripts provided with the *python* tool in the tools diff --git a/doc/src/Intro_overview.rst b/doc/src/Intro_overview.rst index 776002354a497dc1611434e2efd183a5885248b8..df6bfad33d56954dc5371e7204221ac48df9c478 100644 --- a/doc/src/Intro_overview.rst +++ b/doc/src/Intro_overview.rst @@ -15,7 +15,7 @@ that supports the `MPI `_ message-passing library. This includes shared-memory boxes and distributed-memory clusters and supercomputers. -.. _mpi: http://www-unix.mcs.anl.gov/mpi +.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface .. _lws: https://lammps.sandia.gov LAMMPS is written in C++. Earlier versions were written in F77 and diff --git a/doc/src/Intro_website.rst b/doc/src/Intro_website.rst index 125d2e0f4c0e8c3b2e74dc5089e630cab87e194f..7abc78e7e49811a16ff2bc02ee7906aca62941a0 100644 --- a/doc/src/Intro_website.rst +++ b/doc/src/Intro_website.rst @@ -2,22 +2,22 @@ Additional website links ======================== The `LAMMPS website `_ has a variety of additional info about -LAMMPS, beyond what is in this manual. Some of the other pages in -this Intr are included in this list. +LAMMPS, beyond what is in this manual. Some other useful resources +available online are listed below. .. _lws: https://lammps.sandia.gov * `Brief intro and recently added significant features `_ -* `List of features `_ -* `List of non-features `_ +* `List of features `_ +* `List of non-features `_ * `Recent bug fixes and new features `_ * `Download info `_ * `GitHub site `_ * `SourceForge site `_ -* `LAMMPS open-source license `_ +* `LAMMPS open-source license `_ -* `Glossary of MD terms relevant to LAMMPS `_ +* `Glossary of terms relevant to LAMMPS `_ * `LAMMPS highlights with images `_ * `LAMMPS highlights with movies `_ * `Mail list `_ diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index f74965f4f89706a8b5b625bcd3c587338cc1c1af..ba6c40b2554ccb423b292965546b7c041b2ffe48 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -27,9 +27,10 @@ all LAMMPS development is coordinated. The content for this manual is part of the LAMMPS distribution. You can build a local copy of the Manual as HTML pages or a PDF file, by following the steps on the :doc:`Manual build ` doc page. -The manual is split into two parts: -1) :ref:`User documentation ` -and 2) :ref:`Programmer documentation `. +The manual is organized in two parts: +1) A :ref:`User documentation ` for how to install +and use LAMMPS and 2) a :ref:`Programmer documentation ` +for how to write programs using the LAMMPS library or how to modify LAMMPS. ---------- diff --git a/doc/src/Modify.rst b/doc/src/Modify.rst index fa45c4818e69574e4532b5cdccd9eb027dc01224..2a727dfd0fe3ef4af3d93f07fe4c5d93217f51d6 100644 --- a/doc/src/Modify.rst +++ b/doc/src/Modify.rst @@ -8,7 +8,8 @@ this. If you add a new feature to LAMMPS and think it will be of interest to general users, we encourage you to submit it for inclusion in LAMMPS -as a pull request on our `GitHub site `_, after reading the :doc:`Modify contribute ` doc page. +as a pull request on our `GitHub site `_, +after reading :doc:`this page `. .. toctree:: :maxdepth: 1 diff --git a/doc/src/Modify_atom.rst b/doc/src/Modify_atom.rst index 34a529020a274c4a196e5c351f2a8726ce34c06d..5c3a96789e8a12bf3315ea39f49aa4efec0732b0 100644 --- a/doc/src/Modify_atom.rst +++ b/doc/src/Modify_atom.rst @@ -47,13 +47,13 @@ other strings. * - fields_comm - list of properties communicated to ghost atoms every step * - fields_comm_vel - - additional properties communicated if :doc:`comm_modify vel ` is used + - additional properties communicated if :doc:`comm_modify vel ` is used * - fields_reverse - list of properties summed from ghost atoms every step * - fields_border - list of properties communicated with ghost atoms every reneighboring step * - fields_border_vel - - additional properties communicated if :doc:`comm_modify vel ` is used + - additional properties communicated if :doc:`comm_modify vel ` is used * - fields_exchange - list of properties communicated when an atom migrates to another processor * - fields_restart diff --git a/doc/src/Modify_contribute.rst b/doc/src/Modify_contribute.rst index 8bc320a9b007f87f9f28db0dd3bffc690e53dd49..27de36f30c20ef2f26635a54ff955fca6dab115c 100644 --- a/doc/src/Modify_contribute.rst +++ b/doc/src/Modify_contribute.rst @@ -31,14 +31,14 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS you are working on. Only discussions related to LAMMPS development are tolerated, so this is **NOT** for people that look for help with compiling, installing, or using LAMMPS. Please contact the `lammps-users mailing -list `_ for those purposes instead. +list `_ for those purposes instead. How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core codebase, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical -requirements. Once you have prepared everything, see the :doc:`Using -GitHub with LAMMPS Howto ` doc page for instructions on +requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub +Tutorial ` page for instructions on how to submit your changes or new files through a GitHub pull request. If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level @@ -58,8 +58,8 @@ are listed and described on the :doc:`Packages details ` doc p Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See the `Open source `_ page on the LAMMPS -website for details. +used as a license for the rest of LAMMPS. See the :doc:`LAMMPS license +` doc page for details. With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source diff --git a/doc/src/Modify_thermo.rst b/doc/src/Modify_thermo.rst index 564df9ec7ab6b97ca3edfed40fd7f94e4eb1b746..ea09e30c1d1d7fdc431b2fe2cb7ef2aae088358d 100644 --- a/doc/src/Modify_thermo.rst +++ b/doc/src/Modify_thermo.rst @@ -20,7 +20,7 @@ for output. Search for the word "customize" with references to "keyword" in thermo.cpp to see the several locations where code will need to be added. -Note that the :doc:`thermo_style custom ` command already allows +Note that the :doc:`thermo_style custom ` command already allows for thermo output of quantities calculated by :doc:`fixes `, :doc:`computes `, and :doc:`variables `. Thus, it may be simpler to compute what you wish via one of those constructs, than diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 3d21232a8f876b2278143be12835ea2548d4e704..1beeeff5b45d43417fa64ae637338e46a26e5e16 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -299,7 +299,8 @@ Dozens of pair styles and a version of the PPPM long-range Coulombic solver optimized for GPUs. All such styles have a "gpu" as a suffix in their style name. The GPU code can be compiled with either CUDA or OpenCL, however the OpenCL variants are no longer actively maintained -and only the CUDA versions are regularly tested. The :doc:`Speed gpu ` doc page gives details of what hardware and GPU +and only the CUDA versions are regularly tested. The +:doc:`Speed_gpu` page gives details of what hardware and GPU software is required on your system, and details on how to build and use this package. Its styles can be invoked at run time via the "-sf gpu" or "-suffix gpu" :doc:`command-line switches `. See @@ -318,8 +319,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * src/GPU: filenames -> commands * src/GPU/README * lib/gpu/README -* :doc:`Speed packages ` -* :doc:`Speed gpu ` +* :doc:`Accelerator packages ` +* :doc:`GPU package ` * :doc:`Section 2.6 -sf gpu ` * :doc:`Section 2.6 -pk gpu ` * :doc:`package gpu ` @@ -433,7 +434,7 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their -style name. The :doc:`Speed kokkos ` doc page gives +style name. The :doc:`KOKKOS package ` doc page gives details of what hardware and software is required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf kk" or "-suffix kk" :doc:`command-line switches `. Also see the :ref:`GPU `, :ref:`OPT `, @@ -463,8 +464,8 @@ This package has :ref:`specific installation instructions ` on the :doc: * src/KOKKOS: filenames -> commands * src/KOKKOS/README * lib/kokkos/README -* :doc:`Speed packages ` -* :doc:`Speed kokkos ` +* :doc:`Accelerator packages ` +* :doc:`KOKKOS package ` * :doc:`Section 2.6 -k on ... ` * :doc:`Section 2.6 -sf kk ` * :doc:`Section 2.6 -pk kokkos ` @@ -665,7 +666,7 @@ A general interface for machine-learning interatomic potentials. **Install:** -To use this package, also the :ref:`SNAP package` needs to be installed. +To use this package, also the :ref:`SNAP package ` needs to be installed. **Author:** Aidan Thompson (Sandia). @@ -773,7 +774,7 @@ OPT package A handful of pair styles which are optimized for improved CPU performance on single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. The styles have an "opt" suffix in -their style name. The :doc:`Speed opt ` doc page gives +their style name. The :doc:`OPT package ` doc page gives details of how to build and use this package. Its styles can be invoked at run time via the "-sf opt" or "-suffix opt" :doc:`command-line switches `. See also the :ref:`KOKKOS `, :ref:`USER-INTEL `, and :ref:`USER-OMP ` packages, which @@ -789,8 +790,8 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu **Supporting info:** * src/OPT: filenames -> commands -* :doc:`Speed packages ` -* :doc:`Speed opt ` +* :doc:`Accelerator packages ` +* :doc:`OPT package ` * :doc:`Section 2.6 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) * `Benchmarks page `_ of web site @@ -1541,7 +1542,8 @@ USER-INTEL package Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. The :doc:`Speed intel ` doc page gives details of what hardware and +All of them have an "intel" in their style name. The +:doc:`USER-INTEL package ` page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf intel" or "-suffix intel" :doc:`command-line switches `. Also see @@ -1567,8 +1569,8 @@ This package has :ref:`specific installation instructions ` on the : * src/USER-INTEL: filenames -> commands * src/USER-INTEL/README -* :doc:`Speed packages ` -* :doc:`Speed intel ` +* :doc:`Accelerator packages ` +* :doc:`USER-INTEL package ` * :doc:`Section 2.6 -sf intel ` * :doc:`Section 2.6 -pk intel ` * :doc:`package intel ` @@ -1915,7 +1917,7 @@ USER-OMP package Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace styles which are altered to enable threading on many-core CPUs via OpenMP directives. All of them have an "omp" in their style name. -The :doc:`Speed omp ` doc page gives details of what hardware +The :doc:`USER-OMP package ` page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf omp" or "-suffix omp" :doc:`command-line switches `. Also see @@ -1947,8 +1949,8 @@ This package has :ref:`specific installation instructions ` on the :do * src/USER-OMP: filenames -> commands * src/USER-OMP/README -* :doc:`Speed packages ` -* :doc:`Speed omp ` +* :doc:`Accelerator packages ` +* :doc:`USER-OMP package ` * :doc:`Section 2.6 -sf omp ` * :doc:`Section 2.6 -pk omp ` * :doc:`package omp ` diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst index ca22515590ee7c0ba5cc3f6c813ec1b982169b24..ab9be69ab30c38e6c63f241815b1ec8343b48da1 100644 --- a/doc/src/Packages_standard.rst +++ b/doc/src/Packages_standard.rst @@ -37,7 +37,7 @@ package: +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`CORESHELL ` | adiabatic core/shell model | :doc:`Howto coreshell ` | coreshell | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ -| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style dipole/cut ` | dipole | no | +| :ref:`DIPOLE ` | point dipole particles | :doc:`pair_style lj/.../dipole ` | dipole | no | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ | :ref:`GPU ` | GPU-enabled styles | :doc:`Section gpu ` | `Benchmarks `_ | int | +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+ diff --git a/doc/src/Run_basics.rst b/doc/src/Run_basics.rst index d02873a8bebb60d99deea22f898dce3abad6e669..35d5f829a02dd24c3241d91a0d711efc229f41a8 100644 --- a/doc/src/Run_basics.rst +++ b/doc/src/Run_basics.rst @@ -27,11 +27,11 @@ executable itself can be placed elsewhere. As LAMMPS runs it prints info to the screen and a logfile named *log.lammps*\ . More info about output is given on the -:doc:`Run output ` doc page. +:doc:`screen and logfile output ` page. If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING -message and continue. See the :doc:`Errors ` doc page for a +message and continue. See the :doc:`Common Problems ` page for a discussion of the various kinds of errors LAMMPS can or can't detect, a list of all ERROR and WARNING messages, and what to do about them. diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index 054ed66d572a9911274cec6e7ab7cf5b380d5e91..f5435ec3a9523fe74803e2200fbc0617568cee62 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -80,7 +80,7 @@ stdin. Explicitly enable or disable KOKKOS support, as provided by the KOKKOS package. Even if LAMMPS is built with this package, as described -in :doc:`Speed kokkos `, this switch must be set to enable +in the :doc:`the KOKKOS package page `, this switch must be set to enable running with KOKKOS-enabled styles the package provides. If the switch is not set (the default), LAMMPS will operate as if the KOKKOS package were not installed; i.e. you can run standard LAMMPS or with @@ -98,7 +98,8 @@ Either the full word or an abbreviation can be used for the keywords. Note that the keywords do not use a leading minus sign. I.e. the keyword is "t", not "-t". Also note that each of the keywords has a default setting. Examples of when to use these options and what -settings to use on different platforms is given on the :doc:`Speed kokkos ` doc page. +settings to use on different platforms is given on the :doc:`KOKKOS package ` +doc page. * d or device * g or gpus @@ -268,7 +269,7 @@ machine (e.g. your desktop), you can run on more (virtual) processors than you have physical processors. To run multiple independent simulations from one input script, using -multiple partitions, see the :doc:`Howto multiple ` doc +multiple partitions, see the :doc:`Howto multiple ` page. World- and universe-style :doc:`variables ` are useful in this context. @@ -326,7 +327,7 @@ cores within each node are ranked in a desired order. Or when using the :doc:`run_style verlet/split ` command with 2 partitions to insure that a specific Kspace processor (in the second partition) is matched up with a specific set of processors in the first partition. -See the :doc:`Speed tips ` doc page for more details. +See the :doc:`General tips ` page for more details. If the keyword *nth* is used with a setting *N*\ , then it means every Nth processor will be moved to the end of the ranking. This is useful @@ -385,7 +386,7 @@ implementations, either by environment variables that specify how to order physical processors, or by config files that specify what physical processors to assign to each MPI rank. The -reorder switch simply gives you a portable way to do this without relying on MPI -itself. See the :doc:`processors out ` command for how +itself. See the :doc:`processors file ` command for how to output info on the final assignment of physical processors to the LAMMPS simulation domain. @@ -523,10 +524,10 @@ lj/cut/intel, lj/cut/kk, lj/cut/omp, and lj/cut/opt. A variant style can be specified explicitly in your input script, e.g. pair_style lj/cut/gpu. If the -suffix switch is used the specified suffix (gpu,intel,kk,omp,opt) is automatically appended whenever your input -script command creates a new :doc:`atom `, -:doc:`pair `, :doc:`fix `, :doc:`compute `, or -:doc:`run ` style. If the variant version does not exist, -the standard version is created. +script command creates a new :doc:`atom style `, +:doc:`pair style `, :doc:`fix `, +:doc:`compute `, or :doc:`run style `. If the +variant version does not exist, the standard version is created. For the GPU package, using this command-line switch also invokes the default GPU settings, as if the command "package gpu 1" were used at @@ -579,8 +580,8 @@ index variable in the input script, since index variables cannot be re-defined. See the :doc:`variable ` command for more info on defining -index and other kinds of variables and the :doc:`Commands parse ` page for more info on using variables in -input scripts. +index and other kinds of variables and the :doc:`Parsing rules ` +page for more info on using variables in input scripts. .. note:: diff --git a/doc/src/Speed_bench.rst b/doc/src/Speed_bench.rst index 45b5b21d8a9c099ab6106e9699273d2c0c09a58b..66db03e360513830f3e3b37cbcc3bb2a4e4ddfd2 100644 --- a/doc/src/Speed_bench.rst +++ b/doc/src/Speed_bench.rst @@ -38,7 +38,7 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI and bench/KEPLER directories have input files and scripts and instructions for running the same (or similar) problems using OpenMP or GPU or Xeon Phi acceleration options. See the README files in those directories and the -:doc:`Speed packages ` doc pages for instructions on how +:doc:`Accelerator packages ` pages for instructions on how to build LAMMPS and run on that kind of hardware. The bench/POTENTIALS directory has input files which correspond to the diff --git a/doc/src/Speed_kokkos.rst b/doc/src/Speed_kokkos.rst index 3269564d2145a51992591e2062399bc7b8ed4a56..5df53ec2cd3b3983aae283953c4c23ab24edf900 100644 --- a/doc/src/Speed_kokkos.rst +++ b/doc/src/Speed_kokkos.rst @@ -9,7 +9,7 @@ different back end languages such as CUDA, OpenMP, or Pthreads. The Kokkos library also provides data abstractions to adjust (at compile time) the memory layout of data structures like 2d and 3d arrays to optimize performance on different hardware. For more information on -Kokkos, see `GitHub `_. +Kokkos, see `the Kokkos GitHub page `_. The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles that use data structures and macros provided by the Kokkos @@ -20,20 +20,20 @@ including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions see the Kokkos `Wiki `_. -Kokkos currently provides support for 3 modes of execution (per MPI +Kokkos currently provides support for 4 modes of execution (per MPI task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP -(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA -GPUs). You choose the mode at build time to produce an executable -compatible with specific hardware. +(threading for many-core CPUs and Intel Phi), CUDA (for NVIDIA +GPUs) and HIP (for AMD GPUs). You choose the mode at build time to +produce an executable compatible with a specific hardware. -.. note:: +.. admonition:: NVIDIA CUDA support To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit software version 9.0 or later must be installed on your system. See the discussion for the :doc:`GPU package ` for details of how to check and do this. -.. note:: +.. admonition:: CUDA and MPI library compatibility Kokkos with CUDA currently implicitly assumes that the MPI library is CUDA-aware. This is not always the case, especially when using @@ -45,6 +45,13 @@ compatible with specific hardware. LAMMPS command line or by using the command :doc:`package kokkos cuda/aware off ` in the input file. +.. admonition:: AMD GPU support + + To build with Kokkos the HIPCC compiler from the AMD ROCm software + version 3.5 or later is required. Supporting this Kokkos mode in + LAMMPS is still work in progress. Please contact the LAMMPS developers + if you run into problems. + Building LAMMPS with the KOKKOS package """"""""""""""""""""""""""""""""""""""" diff --git a/doc/src/Speed_measure.rst b/doc/src/Speed_measure.rst index 686fdb6adc181ef94b693425541936951663bbeb..1daf49f4c47bda13b6066c5c6910cd3b5e9f9c73 100644 --- a/doc/src/Speed_measure.rst +++ b/doc/src/Speed_measure.rst @@ -14,7 +14,7 @@ timings; you can simply extrapolate from short runs. For the set of runs, look at the timing data printed to the screen and log file at the end of each LAMMPS run. The -:doc:`Run_output ` doc page gives an overview. +:doc:`screen and logfile output ` page gives an overview. Running on one (or a few processors) should give a good estimate of the serial performance and what portions of the timestep are taking diff --git a/doc/src/Speed_omp.rst b/doc/src/Speed_omp.rst index 3d3cb4daf10d126cb33abbe93bd6de29c46d6fc3..f29e3743b4d4cd0065fe3dcb761261c947c38425 100644 --- a/doc/src/Speed_omp.rst +++ b/doc/src/Speed_omp.rst @@ -86,7 +86,8 @@ USER-OMP style (in serial or parallel) with a single thread per MPI task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This is because many of the USER-OMP styles contain similar optimizations -to those used in the OPT package, described in :doc:`Section 5.3.5 `. +to those used in the OPT package, described in +:doc:`the OPT package ` doc page. With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be @@ -95,7 +96,8 @@ specific machine, paying attention to guidelines discussed in the next sub-section. A description of the multi-threading strategy used in the USER-OMP -package and some performance examples are `presented here `_ +package and some performance examples are +`presented here `_. Guidelines for best performance """"""""""""""""""""""""""""""" diff --git a/doc/src/angle_charmm.rst b/doc/src/angle_charmm.rst index 8410f0f8c0e15bbae6d9af38b93758c3fb771442..e557648d9ffd128e887d31dbae0d064548e9a72d 100644 --- a/doc/src/angle_charmm.rst +++ b/doc/src/angle_charmm.rst @@ -1,16 +1,12 @@ .. index:: angle_style charmm +.. index:: angle_style charmm/intel +.. index:: angle_style charmm/kk +.. index:: angle_style charmm/omp angle_style charmm command ========================== -angle_style charmm/intel command -================================ - -angle_style charmm/kk command -============================= - -angle_style charmm/omp command -============================== +Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp* Syntax """""" diff --git a/doc/src/angle_class2.rst b/doc/src/angle_class2.rst index 7d2fdd5d66831578d0fe3238e73b88a0c9a44c21..bf0305055a6b12df373994ba43db0a14a331c32d 100644 --- a/doc/src/angle_class2.rst +++ b/doc/src/angle_class2.rst @@ -1,13 +1,12 @@ .. index:: angle_style class2 +.. index:: angle_style class2/kk +.. index:: angle_style class2/omp +.. index:: angle_style class2/p6 angle_style class2 command ========================== -angle_style class2/kk command -============================= - -angle_style class2/omp command -============================== +Accelerator Variants: *class2/kk*, *class2/omp* angle_style class2/p6 command ============================= diff --git a/doc/src/angle_cosine.rst b/doc/src/angle_cosine.rst index e39e68b2e188e2d3589319472b4d4c908a19bcc1..aea144f7be161d6917bb81f597a8e54b9b3ed1c1 100644 --- a/doc/src/angle_cosine.rst +++ b/doc/src/angle_cosine.rst @@ -1,13 +1,11 @@ .. index:: angle_style cosine +.. index:: angle_style cosine/omp +.. index:: angle_style cosine/kk angle_style cosine command ========================== -angle_style cosine/omp command -============================== - -angle_style cosine/kk command -============================= +Accelerator Variants: *cosine/omp*, *cosine/kk* Syntax """""" diff --git a/doc/src/angle_cosine_delta.rst b/doc/src/angle_cosine_delta.rst index 017b64f8b09c3ba716284f683ea9465e74caa4f8..280e6ea2c49df17427a7a16413e7e69d22bc96c1 100644 --- a/doc/src/angle_cosine_delta.rst +++ b/doc/src/angle_cosine_delta.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/delta +.. index:: angle_style cosine/delta/omp angle_style cosine/delta command ================================ -angle_style cosine/delta/omp command -==================================== +Accelerator Variants: *cosine/delta/omp* Syntax """""" diff --git a/doc/src/angle_cosine_periodic.rst b/doc/src/angle_cosine_periodic.rst index aff4ba2322e097c1d89ae2f0d821c494fc115969..71c2caa3f0a61a5eb7b88d5e1b53660387f1be73 100644 --- a/doc/src/angle_cosine_periodic.rst +++ b/doc/src/angle_cosine_periodic.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/periodic +.. index:: angle_style cosine/periodic/omp angle_style cosine/periodic command =================================== -angle_style cosine/periodic/omp command -======================================= +Accelerator Variants: *cosine/periodic/omp* Syntax """""" diff --git a/doc/src/angle_cosine_shift.rst b/doc/src/angle_cosine_shift.rst index 26603e48be27d9d92e1f2e88c640b01425091ad6..71bda194c70e896c64fab244ef9b115a8244b394 100644 --- a/doc/src/angle_cosine_shift.rst +++ b/doc/src/angle_cosine_shift.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/shift +.. index:: angle_style cosine/shift/omp angle_style cosine/shift command -================================= +================================ -angle_style cosine/shift/omp command -==================================== +Accelerator Variants: *cosine/shift/omp* Syntax """""" diff --git a/doc/src/angle_cosine_shift_exp.rst b/doc/src/angle_cosine_shift_exp.rst index fbdb76aa4565ce5f0cc3d8548d1463c5ff4cbc1b..4ae492875195d6cc83735d4872630e88f0f02b93 100644 --- a/doc/src/angle_cosine_shift_exp.rst +++ b/doc/src/angle_cosine_shift_exp.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/shift/exp +.. index:: angle_style cosine/shift/exp/omp angle_style cosine/shift/exp command ==================================== -angle_style cosine/shift/exp/omp command -======================================== +Accelerator Variants: *cosine/shift/exp/omp* Syntax """""" diff --git a/doc/src/angle_cosine_squared.rst b/doc/src/angle_cosine_squared.rst index 49ddf597411341aa4dc0ad2d941d35c7edc55bdc..4a6a1debe957ad012ec11174b0424a3fec46423f 100644 --- a/doc/src/angle_cosine_squared.rst +++ b/doc/src/angle_cosine_squared.rst @@ -1,10 +1,10 @@ .. index:: angle_style cosine/squared +.. index:: angle_style cosine/squared/omp angle_style cosine/squared command ================================== -angle_style cosine/squared/omp command -====================================== +Accelerator Variants: *cosine/squared/omp* Syntax """""" diff --git a/doc/src/angle_cross.rst b/doc/src/angle_cross.rst index 5769e756c3f2e06e32c89d90a43658d95544b3fc..3cd1884be0dadd8c7eac50356490426139609afe 100644 --- a/doc/src/angle_cross.rst +++ b/doc/src/angle_cross.rst @@ -1,7 +1,7 @@ .. index:: angle_style cross angle_style cross command -========================== +========================= Syntax """""" diff --git a/doc/src/angle_dipole.rst b/doc/src/angle_dipole.rst index 3b4e4f530436b59f451a52fd5907e1da037d46b8..4dd8aadfb814e7c78d27e8ba84cd9c17a3df684b 100644 --- a/doc/src/angle_dipole.rst +++ b/doc/src/angle_dipole.rst @@ -1,10 +1,10 @@ .. index:: angle_style dipole +.. index:: angle_style dipole/omp angle_style dipole command ========================== -angle_style dipole/omp command -============================== +Accelerator Variants: *dipole/omp* Syntax """""" diff --git a/doc/src/angle_fourier.rst b/doc/src/angle_fourier.rst index cbe654427119d9ef812921e74d05983a4aa6220c..231f45e808dc5e84079f556f8d72ce37430282ca 100644 --- a/doc/src/angle_fourier.rst +++ b/doc/src/angle_fourier.rst @@ -1,10 +1,10 @@ .. index:: angle_style fourier +.. index:: angle_style fourier/omp angle_style fourier command =========================== -angle_style fourier/omp command -=============================== +Accelerator Variants: *fourier/omp* Syntax """""" diff --git a/doc/src/angle_fourier_simple.rst b/doc/src/angle_fourier_simple.rst index b36f69cbec697c489b7253c31d3d92151c1ba8dd..14b4bbcfe934c02c7c82137312f289f5ee2feafa 100644 --- a/doc/src/angle_fourier_simple.rst +++ b/doc/src/angle_fourier_simple.rst @@ -1,10 +1,10 @@ .. index:: angle_style fourier/simple +.. index:: angle_style fourier/simple/omp angle_style fourier/simple command ================================== -angle_style fourier/simple/omp command -====================================== +Accelerator Variants: *fourier/simple/omp* Syntax """""" diff --git a/doc/src/angle_harmonic.rst b/doc/src/angle_harmonic.rst index c6ad93c3ec0a8912617c29b19a563ccac9d0e5b9..06cf1d460bb235982459f535c9916f90cde73d0a 100644 --- a/doc/src/angle_harmonic.rst +++ b/doc/src/angle_harmonic.rst @@ -1,16 +1,12 @@ .. index:: angle_style harmonic +.. index:: angle_style harmonic/intel +.. index:: angle_style harmonic/kk +.. index:: angle_style harmonic/omp angle_style harmonic command ============================ -angle_style harmonic/intel command -================================== - -angle_style harmonic/kk command -=============================== - -angle_style harmonic/omp command -================================ +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/angle_quartic.rst b/doc/src/angle_quartic.rst index 71297e60a0ff95f595ff441c8678c8535f9c0cdc..7dfb4b2896374f917f67acf350f69288474589f4 100644 --- a/doc/src/angle_quartic.rst +++ b/doc/src/angle_quartic.rst @@ -1,10 +1,10 @@ .. index:: angle_style quartic +.. index:: angle_style quartic/omp angle_style quartic command =========================== -angle_style quartic/omp command -=============================== +Accelerator Variants: *quartic/omp* Syntax """""" diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_sdk.rst index f5583d5013ecc480e11bc1ebe577488a33f77ee7..340a3e4de74c6555f96ec285c3bd8279f3b82f9f 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_sdk.rst @@ -1,10 +1,10 @@ .. index:: angle_style sdk +.. index:: angle_style sdk/omp angle_style sdk command ======================= -angle_style sdk/omp command -=========================== +Accelerator Variants: *sdk/omp* Syntax """""" diff --git a/doc/src/angle_table.rst b/doc/src/angle_table.rst index d8d9476620f9a8f64a965aeed4b3b4018f60e310..cad9f5a82fa4ce1e262bf94a9bf58d91b4d69496 100644 --- a/doc/src/angle_table.rst +++ b/doc/src/angle_table.rst @@ -1,10 +1,10 @@ .. index:: angle_style table +.. index:: angle_style table/omp angle_style table command ========================= -angle_style table/omp command -============================= +Accelerator Variants: *table/omp* Syntax """""" diff --git a/doc/src/bond_class2.rst b/doc/src/bond_class2.rst index 41eb2b4e50f41a2892d9ae7255eaf42c1dbd61c6..aea503738fbbb5600da906cddcdecd91778e65a5 100644 --- a/doc/src/bond_class2.rst +++ b/doc/src/bond_class2.rst @@ -1,13 +1,11 @@ .. index:: bond_style class2 +.. index:: bond_style class2/omp +.. index:: bond_style class2/kk bond_style class2 command ========================= -bond_style class2/omp command -============================= - -bond_style class2/kk command -============================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index 8ec117bf24c76b105e7c6f69e69bbb6e27fed881..0c6a37ca62e1eced05fc31748c0bc572f7188a7e 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -1,16 +1,12 @@ .. index:: bond_style fene +.. index:: bond_style fene/intel +.. index:: bond_style fene/kk +.. index:: bond_style fene/omp bond_style fene command ======================= -bond_style fene/intel command -============================= - -bond_style fene/kk command -========================== - -bond_style fene/omp command -=========================== +Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp* Syntax """""" diff --git a/doc/src/bond_fene_expand.rst b/doc/src/bond_fene_expand.rst index 5bcb409238103a1c88328a56c19403c9be1eef3b..1be06561e9448e30317c5ae0cb48e8f3d232dac6 100644 --- a/doc/src/bond_fene_expand.rst +++ b/doc/src/bond_fene_expand.rst @@ -1,10 +1,10 @@ .. index:: bond_style fene/expand +.. index:: bond_style fene/expand/omp bond_style fene/expand command ============================== -bond_style fene/expand/omp command -================================== +Accelerator Variants: *fene/expand/omp* Syntax """""" diff --git a/doc/src/bond_gromos.rst b/doc/src/bond_gromos.rst index f09e5761fe4b17ce2e4bf65533b3eafd4a9755ee..d4eb958ebe6a888ecb1ae2e02f8216b523fa23cc 100644 --- a/doc/src/bond_gromos.rst +++ b/doc/src/bond_gromos.rst @@ -1,10 +1,10 @@ .. index:: bond_style gromos +.. index:: bond_style gromos/omp bond_style gromos command ========================= -bond_style gromos/omp command -============================= +Accelerator Variants: *gromos/omp* Syntax """""" diff --git a/doc/src/bond_harmonic.rst b/doc/src/bond_harmonic.rst index eaa1ee798650b325f64f4009814620b81eb16619..e3320f2e19952bfda264e70bf7026a1592a60a3f 100644 --- a/doc/src/bond_harmonic.rst +++ b/doc/src/bond_harmonic.rst @@ -1,16 +1,12 @@ .. index:: bond_style harmonic +.. index:: bond_style harmonic/intel +.. index:: bond_style harmonic/kk +.. index:: bond_style harmonic/omp bond_style harmonic command =========================== -bond_style harmonic/intel command -================================= - -bond_style harmonic/kk command -============================== - -bond_style harmonic/omp command -=============================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/bond_harmonic_shift.rst b/doc/src/bond_harmonic_shift.rst index c124bacf0f93f530af6bc19755648c343b19513b..469c37096908226f5962352de3c61c77e650a52f 100644 --- a/doc/src/bond_harmonic_shift.rst +++ b/doc/src/bond_harmonic_shift.rst @@ -1,10 +1,10 @@ .. index:: bond_style harmonic/shift +.. index:: bond_style harmonic/shift/omp bond_style harmonic/shift command ================================= -bond_style harmonic/shift/omp command -===================================== +Accelerator Variants: *harmonic/shift/omp* Syntax """""" diff --git a/doc/src/bond_harmonic_shift_cut.rst b/doc/src/bond_harmonic_shift_cut.rst index e1b7e990d45af1bb01a05c5a95cae0a139539cd2..d0f44740b3e1b1f008046579c0c14baf3d000465 100644 --- a/doc/src/bond_harmonic_shift_cut.rst +++ b/doc/src/bond_harmonic_shift_cut.rst @@ -1,10 +1,10 @@ .. index:: bond_style harmonic/shift/cut +.. index:: bond_style harmonic/shift/cut/omp bond_style harmonic/shift/cut command ===================================== -bond_style harmonic/shift/cut/omp command -========================================= +Accelerator Variants: *harmonic/shift/cut/omp* Syntax """""" diff --git a/doc/src/bond_morse.rst b/doc/src/bond_morse.rst index 64fc61298a37fc43040085b857dd23d686c8224c..f096624ba09d45960eeb24f8d9631be5d47f9c43 100644 --- a/doc/src/bond_morse.rst +++ b/doc/src/bond_morse.rst @@ -1,10 +1,10 @@ .. index:: bond_style morse +.. index:: bond_style morse/omp bond_style morse command ======================== -bond_style morse/omp command -============================ +Accelerator Variants: *morse/omp* Syntax """""" diff --git a/doc/src/bond_nonlinear.rst b/doc/src/bond_nonlinear.rst index 75ab4ad347c7fc58844fc88710b2134004fa6c02..77271502ea52c78a22f706aeb451960caa4b2e3f 100644 --- a/doc/src/bond_nonlinear.rst +++ b/doc/src/bond_nonlinear.rst @@ -1,10 +1,10 @@ .. index:: bond_style nonlinear +.. index:: bond_style nonlinear/omp bond_style nonlinear command ============================ -bond_style nonlinear/omp command -================================ +Accelerator Variants: *nonlinear/omp* Syntax """""" diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index ada2f0e1ed70d3a54888d6a257c8471ea953c64f..3f52424d49351d83e2c82697763ed158a024680d 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -1,4 +1,6 @@ .. index:: bond_style oxdna/fene +.. index:: bond_style oxdna2/fene +.. index:: bond_style oxrna2/fene bond_style oxdna/fene command ============================= diff --git a/doc/src/bond_quartic.rst b/doc/src/bond_quartic.rst index d54c19bbd47681c48829ccab57f01b665f105151..8c5b363e5472fd3bf28863f9357f4deb0b0dfdb0 100644 --- a/doc/src/bond_quartic.rst +++ b/doc/src/bond_quartic.rst @@ -1,10 +1,10 @@ .. index:: bond_style quartic +.. index:: bond_style quartic/omp bond_style quartic command ========================== -bond_style quartic/omp command -============================== +Accelerator Variants: *quartic/omp* Syntax """""" diff --git a/doc/src/bond_special.rst b/doc/src/bond_special.rst index bd93bb644cbb67cec0ca3153b1078d3cfa81de15..d2423c9e230e4494854e44134599fb1c4a1c0673 100644 --- a/doc/src/bond_special.rst +++ b/doc/src/bond_special.rst @@ -1,7 +1,7 @@ .. index:: bond_style special bond_style special command -================================= +========================== Syntax """""" diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 9f8ebacef05266e86d688db8df78f8c732694b78..fedb50355d406b12c8bdfdbb8cbcf89602f9b51d 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -1,10 +1,10 @@ .. index:: bond_style table +.. index:: bond_style table/omp bond_style table command ======================== -bond_style table/omp command -============================ +Accelerator Variants: *table/omp* Syntax """""" diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index 77149306dc56d24ff66fe44fb50fff25b6832c87..ab47aed9b38e72396484774fbe0a99e3bbfd6900 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -1,4 +1,6 @@ .. index:: compute cluster/atom +.. index:: compute fragment/atom +.. index:: compute aggregate/atom compute cluster/atom command ============================ diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index cbf879b8bda7750cefeac229cdc20241cbaa62c6..f3c6f818aff220c0557beb802cf29d1d28d64229 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -1,10 +1,10 @@ .. index:: compute coord/atom +.. index:: compute coord/atom/kk compute coord/atom command ========================== -compute coord/atom/kk command -=================================== +Accelerator Variants: *coord/atom/kk* Syntax """""" diff --git a/doc/src/compute_mesont.rst b/doc/src/compute_mesont.rst index bf0ade16c1cb326883fc23e26d05f8d1c17e7c20..44d6054e223e3a7b3ab1683f8b45d55716620412 100644 --- a/doc/src/compute_mesont.rst +++ b/doc/src/compute_mesont.rst @@ -1,7 +1,7 @@ .. index:: compute mesont compute mesont command -========================== +====================== Syntax """""" diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index c8ab4d7b9b1d1581fb1a270c07eba4425732e710..2a36fb4cc0fd70a86bdbb43a6d73f8384c34db29 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -1,10 +1,10 @@ .. index:: compute orientorder/atom +.. index:: compute orientorder/atom/kk compute orientorder/atom command ================================ -compute orientorder/atom/kk command -=================================== +Accelerator Variants: *orientorder/atom/kk* Syntax """""" diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index bf7d0dc28c49cfb74ba5de13de684ded4a559309..c7815305c0b147e08a9df4f13e98ed1f016708ec 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -1,4 +1,5 @@ .. index:: compute reduce +.. index:: compute reduce/region compute reduce command ====================== diff --git a/doc/src/compute_smd_ulsph_effm.rst b/doc/src/compute_smd_ulsph_effm.rst index e6d6b772a001b747895b1a5f56a6a1e605862a37..ff12f9cdac65510fb9ef3d34af2bf0e7391b1320 100644 --- a/doc/src/compute_smd_ulsph_effm.rst +++ b/doc/src/compute_smd_ulsph_effm.rst @@ -1,7 +1,7 @@ .. index:: compute smd/ulsph/effm compute smd/ulsph/effm command -================================ +============================== Syntax """""" diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 7e74a1bd61124df315d03f63e222eef5dd86c685..08b06a32ec853173b79ec2e01b27d762a01f24ed 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -1,4 +1,7 @@ .. index:: compute sna/atom +.. index:: compute snad/atom +.. index:: compute snav/atom +.. index:: compute snap compute sna/atom command ======================== diff --git a/doc/src/compute_sph_e_atom.rst b/doc/src/compute_sph_e_atom.rst index 08378c7c992bde33ecee122d3a005a83cac55587..17591257f28a05ddc89f4b9c3e02a5ab4007ca24 100644 --- a/doc/src/compute_sph_e_atom.rst +++ b/doc/src/compute_sph_e_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/e/atom compute sph/e/atom command -=========================== +========================== Syntax """""" diff --git a/doc/src/compute_sph_rho_atom.rst b/doc/src/compute_sph_rho_atom.rst index 975ebf996dde68e4fcaf0979d280e6a28798fe77..c422a5ecbb491044d5272b76578c08e4fe61afef 100644 --- a/doc/src/compute_sph_rho_atom.rst +++ b/doc/src/compute_sph_rho_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/rho/atom compute sph/rho/atom command -============================= +============================ Syntax """""" diff --git a/doc/src/compute_sph_t_atom.rst b/doc/src/compute_sph_t_atom.rst index 2f8ad12f45dfeaa1bd824a735b0d287b89f44f8b..922adfff58dd1fcdf62d32e268e0dea92fb00363 100644 --- a/doc/src/compute_sph_t_atom.rst +++ b/doc/src/compute_sph_t_atom.rst @@ -1,7 +1,7 @@ .. index:: compute sph/t/atom compute sph/t/atom command -=========================== +========================== Syntax """""" diff --git a/doc/src/compute_stress_atom.rst b/doc/src/compute_stress_atom.rst index 2bdab03bda0ae0d0eaf468d8da9efcbf0d205900..16afd49548173c02daebc890c1a97a3ef7bad227 100644 --- a/doc/src/compute_stress_atom.rst +++ b/doc/src/compute_stress_atom.rst @@ -1,4 +1,5 @@ .. index:: compute stress/atom +.. index:: compute centroid/stress/atom compute stress/atom command =========================== diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst index 4d0d21cb870f7dc8659b5b5188098b4e6cc070b9..f164a33c2662d44e0848b18ef6485cf5400be241 100644 --- a/doc/src/compute_stress_mop.rst +++ b/doc/src/compute_stress_mop.rst @@ -1,4 +1,5 @@ .. index:: compute stress/mop +.. index:: compute stress/mop/profile compute stress/mop command ========================== diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 281425763ac527f085d1ebd6d402bf6c2b61457b..64876185168308afd8f009ee91b73e0550595449 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -1,4 +1,8 @@ .. index:: compute force/tally +.. index:: compute heat/flux/tally +.. index:: compute pe/tally +.. index:: compute pe/mol/tally +.. index:: compute stress/tally compute force/tally command =========================== diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index ac11aa155c2af01a6d77ba415c3d15e56b068ec6..a82046367e95392edce475fa0f1cf1aa36d00047 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -1,10 +1,10 @@ .. index:: compute temp +.. index:: compute temp/kk compute temp command ==================== -compute temp/kk command -======================= +Accelerator Variants: *temp/kk* Syntax """""" diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index bbaaaf2dd4cdcf5242f84c7bb550451d91b3d2cf..9588cf8272f87e699b9f060eec2e5bc60bff1ad0 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -1,16 +1,13 @@ .. index:: dihedral_style charmm +.. index:: dihedral_style charmm/intel +.. index:: dihedral_style charmm/kk +.. index:: dihedral_style charmm/omp +.. index:: dihedral_style charmmfsw dihedral_style charmm command ============================= -dihedral_style charmm/intel command -=================================== - -dihedral_style charmm/kk command -================================ - -dihedral_style charmm/omp command -================================= +Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp* dihedral_style charmmfsw command ================================ diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index 907102a4f651c2e284bc3811dceede3f4ade553d..a98cf6b041ba78c599315fcabeb710513cecf694 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -1,13 +1,11 @@ .. index:: dihedral_style class2 +.. index:: dihedral_style class2/omp +.. index:: dihedral_style class2/kk dihedral_style class2 command ============================= -dihedral_style class2/omp command -================================= - -dihedral_style class2/kk command -================================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index 9648bc538788d4ce35952afd9349d43b2cff3776..1f0195df8336fd6ee192c4b7a56cd21fd6a74d24 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style cosine/shift/exp +.. index:: dihedral_style cosine/shift/exp/omp dihedral_style cosine/shift/exp command ======================================= -dihedral_style cosine/shift/exp/omp command -=========================================== +Accelerator Variants: *cosine/shift/exp/omp* Syntax """""" diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index d795488107a491f0d022024bf3649f91f8380585..f55011c90273222db116b748167e8b1e2153cffe 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -1,13 +1,11 @@ .. index:: dihedral_style fourier +.. index:: dihedral_style fourier/intel +.. index:: dihedral_style fourier/omp dihedral_style fourier command ============================== -dihedral_style fourier/intel command -==================================== - -dihedral_style fourier/omp command -================================== +Accelerator Variants: *fourier/intel*, *fourier/omp* Syntax """""" diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index f6e9794d3e6320680d17e33139d8929f90b2eb87..0ee6339ea0d057915bc92ef3afadef7a79ceba3e 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -1,16 +1,12 @@ .. index:: dihedral_style harmonic +.. index:: dihedral_style harmonic/intel +.. index:: dihedral_style harmonic/kk +.. index:: dihedral_style harmonic/omp dihedral_style harmonic command =============================== -dihedral_style harmonic/intel command -===================================== - -dihedral_style harmonic/kk command -================================== - -dihedral_style harmonic/omp command -=================================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 58738dd7a7c42f364bdd08f5ba8d873452594306..89258cff35707528c3bf34a060ace79d79339bfc 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style helix +.. index:: dihedral_style helix/omp dihedral_style helix command ============================ -dihedral_style helix/omp command -================================ +Accelerator Variants: *helix/omp* Syntax """""" diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index c13d45863f6ff3bc806eb550e6ec5e813f2b19ef..176d3815dca31d4711e46fb63e578b014842ab81 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style multi/harmonic +.. index:: dihedral_style multi/harmonic/omp dihedral_style multi/harmonic command ===================================== -dihedral_style multi/harmonic/omp command -========================================= +Accelerator Variants: *multi/harmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index e2223382e22ce6f59caed4b9794c39528abbeaea..24119031267d0435edee8dc119941e42f7a0d734 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style nharmonic +.. index:: dihedral_style nharmonic/omp dihedral_style nharmonic command -================================= +================================ -dihedral_style nharmonic/omp command -===================================== +Accelerator Variants: *nharmonic/omp* Syntax """""" diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index a2be0b5b2d2eed6f2c7a68bde7b80596830a145c..36b1897fce7f65cd174f484d587f2fbeb6388f9e 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -1,16 +1,12 @@ .. index:: dihedral_style opls +.. index:: dihedral_style opls/intel +.. index:: dihedral_style opls/kk +.. index:: dihedral_style opls/omp dihedral_style opls command =========================== -dihedral_style opls/intel command -================================= - -dihedral_style opls/kk command -============================== - -dihedral_style opls/omp command -=============================== +Accelerator Variants: *opls/intel*, *opls/kk*, *opls/omp* Syntax """""" diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 9c4a7075624047f19ca3104931b67a2ebab49df8..dbe680fc8268c5fa7758652ed148ff98b8782d98 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style quadratic +.. index:: dihedral_style quadratic/omp dihedral_style quadratic command ================================ -dihedral_style quadratic/omp command -==================================== +Accelerator Variants: *quadratic/omp* Syntax """""" diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 9ed7249572adf381bfe45fe240fe0e762b1bbb30..ff3e61baeedd977d81c15b95cbb359acee9451bd 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -1,10 +1,10 @@ .. index:: dihedral_style table +.. index:: dihedral_style table/omp dihedral_style table command ============================ -dihedral_style table/omp command -================================ +Accelerator Variants: *table/omp* Syntax """""" diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 3df68edfd5679effd63d767304bca12d9ccea35f..0f481f917de3c80389fd01b54746a350c99f7cac 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -1,7 +1,7 @@ .. index:: dihedral_style zero dihedral_style zero command -============================ +=========================== Syntax """""" diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 7c4ef88fd6e340e4fde161e027015e85307dc877..d50112ac488c5b96a7ac3f03b2a8437a6d61ea6a 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -1,4 +1,5 @@ .. index:: fix ave/histo +.. index:: fix ave/histo/weight fix ave/histo command ===================== diff --git a/doc/src/fix_bond_create.rst b/doc/src/fix_bond_create.rst index d0c7fb985ca362bd895ba6553fd464a05cd683f7..34f0d19f8d693c3edb389b3fbd79cec1dbb5cce5 100644 --- a/doc/src/fix_bond_create.rst +++ b/doc/src/fix_bond_create.rst @@ -1,4 +1,5 @@ .. index:: fix bond/create +.. index:: fix bond/create/angle fix bond/create command ======================= diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 70b15f0d796f748303d52d73ee949ded24c21528..999a88c4e73e7a64e3ccab6ec1a4942765d7b9c1 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -1,10 +1,10 @@ .. index:: fix deform +.. index:: fix deform/kk fix deform command ================== -fix deform/kk command -===================== +Accelerator Variants: *deform/kk* Syntax """""" diff --git a/doc/src/fix_dpd_energy.rst b/doc/src/fix_dpd_energy.rst index 6d510f182570f88b114d0e8a662d7a64b4609ed1..732f99b516c5eb5168b3abc0f7f2fda52063d6af 100644 --- a/doc/src/fix_dpd_energy.rst +++ b/doc/src/fix_dpd_energy.rst @@ -1,10 +1,10 @@ .. index:: fix dpd/energy +.. index:: fix dpd/energy/kk fix dpd/energy command ====================== -fix dpd/energy/kk command -========================= +Accelerator Variants: *dpd/energy/kk* Syntax """""" diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index 4373645c84d1edd7f2004e6933cf2a0bbe4fbcae..29bbc92f78c5021113ccb97cb94d72e41859278a 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -1,4 +1,5 @@ .. index:: fix edpd/source +.. index:: fix tdpd/source fix edpd/source command ======================= diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index bda2d25b1fd577e8de29af1395235ebbe476bfc7..792b041576d9237d8889a4b99faf5e2259c9a5b0 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -1,4 +1,5 @@ .. index:: fix drude/transform/direct +.. index:: fix drude/transform/inverse fix drude/transform/direct command ================================== diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index e92011cb11215969b5ed1ee7a52e6977b275525e..7c6ef750892063c1da20761384cf2556cdc06825 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -1,10 +1,10 @@ .. index:: fix enforce2d +.. index:: fix enforce2d/kk fix enforce2d command ===================== -fix enforce2d/kk command -======================== +Accelerator Variants: *enforce2d/kk* Syntax """""" diff --git a/doc/src/fix_eos_table_rx.rst b/doc/src/fix_eos_table_rx.rst index bd13398e0abfc35371fa40292dcad9d4bc180bef..56bde44d986fb5cee97583f675db64b8dc8b051c 100644 --- a/doc/src/fix_eos_table_rx.rst +++ b/doc/src/fix_eos_table_rx.rst @@ -1,10 +1,10 @@ .. index:: fix eos/table/rx +.. index:: fix eos/table/rx/kk fix eos/table/rx command ======================== -fix eos/table/rx/kk command -=========================== +Accelerator Variants: *eos/table/rx/kk* Syntax """""" diff --git a/doc/src/fix_freeze.rst b/doc/src/fix_freeze.rst index f81954ff5dfe7e812d27e7b4a0bd5467e2d3223b..a7370c7f445dbc97fac53debc41ddca2593b0fc4 100644 --- a/doc/src/fix_freeze.rst +++ b/doc/src/fix_freeze.rst @@ -1,10 +1,10 @@ .. index:: fix freeze +.. index:: fix freeze/kk fix freeze command ================== -fix freeze/kk command -===================== +Accelerator Variants: *freeze/kk* Syntax """""" diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 5f06f6d22a2f8803b8eea11003e8f30b21b30208..a163eb4ab2ecfef098bd2eda6101e9da20084263 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -1,13 +1,11 @@ .. index:: fix gravity +.. index:: fix gravity/omp +.. index:: fix gravity/kk fix gravity command =================== -fix gravity/omp command -======================= - -fix gravity/kk command -====================== +Accelerator Variants: *gravity/omp*, *gravity/kk* Syntax """""" diff --git a/doc/src/fix_langevin.rst b/doc/src/fix_langevin.rst index 80f49642423c71079cb566c87155f1b55d87ec38..e31434247f08018bcbe262fce562504a501f9dff 100644 --- a/doc/src/fix_langevin.rst +++ b/doc/src/fix_langevin.rst @@ -1,10 +1,10 @@ .. index:: fix langevin +.. index:: fix langevin/kk fix langevin command ==================== -fix langevin/kk command -======================= +Accelerator Variants: *langevin/kk* Syntax """""" diff --git a/doc/src/fix_momentum.rst b/doc/src/fix_momentum.rst index ca6e19005e3cb016acc33a833752acf337babc09..393a6a16cd4007572133b9da3ba67917ea938d70 100644 --- a/doc/src/fix_momentum.rst +++ b/doc/src/fix_momentum.rst @@ -1,10 +1,11 @@ .. index:: fix momentum +.. index:: fix momentum/kk +.. index:: fix momentum/chunk fix momentum command ==================== -fix momentum/kk command -======================= +Accelerator Variants: *momentum/kk* fix momentum/chunk command ========================== diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index c7e9b64c962dfe3de88240c5444adfb8b7ccbd77..d0df1bd0f9556b856ecfaf3739735bf8d7a1e747 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -1,4 +1,6 @@ .. index:: fix mvv/dpd +.. index:: fix mvv/edpd +.. index:: fix mvv/tdpd fix mvv/dpd command =================== diff --git a/doc/src/fix_nh.rst b/doc/src/fix_nh.rst index 64a3c3b0611c7d6895085814087f463a397c7fa2..84b497dc3f7e6ba936f831e085e8bc50adf92ca6 100644 --- a/doc/src/fix_nh.rst +++ b/doc/src/fix_nh.rst @@ -1,37 +1,29 @@ .. index:: fix nvt +.. index:: fix nvt/intel +.. index:: fix nvt/kk +.. index:: fix nvt/omp +.. index:: fix npt +.. index:: fix npt/intel +.. index:: fix npt/kk +.. index:: fix npt/omp +.. index:: fix nph +.. index:: fix nph/kk +.. index:: fix nph/omp fix nvt command =============== -fix nvt/intel command -===================== - -fix nvt/kk command -================== - -fix nvt/omp command -=================== +Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp* fix npt command =============== -fix npt/intel command -===================== - -fix npt/kk command -================== - -fix npt/omp command -=================== +Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp* fix nph command =============== -fix nph/kk command -================== - -fix nph/omp command -=================== +Accelerator Variants: *nph/kk*, *nph/omp* Syntax """""" diff --git a/doc/src/fix_nh_eff.rst b/doc/src/fix_nh_eff.rst index 4d4d536ac22b7b2fa0df3229c90eda39dcc703e7..3e54ed97657664a7b639b5f8bf153fc22aac3ae9 100644 --- a/doc/src/fix_nh_eff.rst +++ b/doc/src/fix_nh_eff.rst @@ -1,4 +1,6 @@ .. index:: fix nvt/eff +.. index:: fix npt/eff +.. index:: fix nph/eff fix nvt/eff command =================== diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index 272f84d5208ab26d07a1527f539dae7f46ccd01c..1c1e7a11d2648632746d6794bb0ca72c89833922 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -1,4 +1,5 @@ .. index:: fix nvt/uef +.. index:: fix npt/uef fix nvt/uef command =================== diff --git a/doc/src/fix_nph_asphere.rst b/doc/src/fix_nph_asphere.rst index 2e5dd16c8f9c44a452393a9e19f58c84f152290f..da0510492ece4302a30dd0e5dfde3e175c283275 100644 --- a/doc/src/fix_nph_asphere.rst +++ b/doc/src/fix_nph_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nph/asphere +.. index:: fix nph/asphere/omp fix nph/asphere command ======================= -fix nph/asphere/omp command -=========================== +Accelerator Variants: *nph/asphere/omp* Syntax """""" diff --git a/doc/src/fix_nph_sphere.rst b/doc/src/fix_nph_sphere.rst index efa6ca38b5636ffbaf8a9543a70671e1e4a67841..4b76f7252f3af807f6ae86e41c4a88ec2fcb4209 100644 --- a/doc/src/fix_nph_sphere.rst +++ b/doc/src/fix_nph_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix nph/sphere +.. index:: fix nph/sphere/omp fix nph/sphere command ====================== -fix nph/sphere/omp command -========================== +Accelerator Variants: *nph/sphere/omp* Syntax """""" diff --git a/doc/src/fix_nphug.rst b/doc/src/fix_nphug.rst index c46e98fe3eb3c37e4c0ea46eb14f223fd9ee91b7..d55f435d435c79929dae276ac05170d6662b3c0e 100644 --- a/doc/src/fix_nphug.rst +++ b/doc/src/fix_nphug.rst @@ -1,10 +1,10 @@ .. index:: fix nphug +.. index:: fix nphug/omp fix nphug command ================= -fix nphug/omp command -===================== +Accelerator Variants: *nphug/omp* Syntax """""" diff --git a/doc/src/fix_npt_asphere.rst b/doc/src/fix_npt_asphere.rst index 5537365359293afa791e5117ae6ae70372e093f9..de2289a0689849b66483220c6d92ffa05bc2bcc3 100644 --- a/doc/src/fix_npt_asphere.rst +++ b/doc/src/fix_npt_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix npt/asphere +.. index:: fix npt/asphere/omp fix npt/asphere command ======================= -fix npt/asphere/omp command -=========================== +Accelerator Variants: *npt/asphere/omp* Syntax """""" diff --git a/doc/src/fix_npt_sphere.rst b/doc/src/fix_npt_sphere.rst index 4e8188ac0c8a836bc7bfd2e24cd9b0b20bb6a611..7363375ff38d4976ae59c6045c97e0497ec490ad 100644 --- a/doc/src/fix_npt_sphere.rst +++ b/doc/src/fix_npt_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix npt/sphere +.. index:: fix npt/sphere/omp fix npt/sphere command ====================== -fix npt/sphere/omp command -========================== +Accelerator Variants: *npt/sphere/omp* Syntax """""" diff --git a/doc/src/fix_numdiff.rst b/doc/src/fix_numdiff.rst index 0c4f731ea08fc735cdf1cb2845ec3fccbf689c32..22c1c59748fc3ab3a795e0f0b74e25256b90a84a 100644 --- a/doc/src/fix_numdiff.rst +++ b/doc/src/fix_numdiff.rst @@ -1,7 +1,7 @@ .. index:: fix numdiff fix numdiff command -==================== +=================== Syntax """""" diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index 0026d38e8c21abc25810d7b163a6e441bcbc23f6..71f8ec300f04208808d1611914b4bd30c5b94282 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -1,16 +1,12 @@ .. index:: fix nve +.. index:: fix nve/intel +.. index:: fix nve/kk +.. index:: fix nve/omp fix nve command =============== -fix nve/intel command -===================== - -fix nve/kk command -================== - -fix nve/omp command -=================== +Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp* Syntax """""" diff --git a/doc/src/fix_nve_asphere.rst b/doc/src/fix_nve_asphere.rst index f1441fdd3c60e3bd5d122b43d5e8208c016ce58e..af80460b326b67ec5794364abc082c0cd7d4bbcb 100644 --- a/doc/src/fix_nve_asphere.rst +++ b/doc/src/fix_nve_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nve/asphere +.. index:: fix nve/asphere/intel fix nve/asphere command ======================= -fix nve/asphere/intel command -============================= +Accelerator Variants: *nve/asphere/intel* Syntax """""" diff --git a/doc/src/fix_nve_sphere.rst b/doc/src/fix_nve_sphere.rst index 59d951782a2b0c15627519cd59b0688b612c6028..0230255b4291bf832354e41c120692e8dab1cc2e 100644 --- a/doc/src/fix_nve_sphere.rst +++ b/doc/src/fix_nve_sphere.rst @@ -1,13 +1,11 @@ .. index:: fix nve/sphere +.. index:: fix nve/sphere/omp +.. index:: fix nve/sphere/kk fix nve/sphere command ====================== -fix nve/sphere/omp command -========================== - -fix nve/sphere/kk command -========================= +Accelerator Variants: *nve/sphere/omp*, *nve/sphere/kk* Syntax """""" diff --git a/doc/src/fix_nvt_asphere.rst b/doc/src/fix_nvt_asphere.rst index a08dae765c81ceb7bd9e0ee08a5554c63f66c088..bb4139d95f9736df90e64c65dadbb2749d69d237 100644 --- a/doc/src/fix_nvt_asphere.rst +++ b/doc/src/fix_nvt_asphere.rst @@ -1,10 +1,10 @@ .. index:: fix nvt/asphere +.. index:: fix nvt/asphere/omp fix nvt/asphere command ======================= -fix nvt/asphere/omp command -=========================== +Accelerator Variants: *nvt/asphere/omp* Syntax """""" diff --git a/doc/src/fix_nvt_sllod.rst b/doc/src/fix_nvt_sllod.rst index b5051b86927ad2afb2197f598132dfd68ea15e41..ff9a4f0d1290c7b63145b31ad9ab39a4b8e75d1f 100644 --- a/doc/src/fix_nvt_sllod.rst +++ b/doc/src/fix_nvt_sllod.rst @@ -1,13 +1,11 @@ .. index:: fix nvt/sllod +.. index:: fix nvt/sllod/intel +.. index:: fix nvt/sllod/omp fix nvt/sllod command ===================== -fix nvt/sllod/intel command -=========================== - -fix nvt/sllod/omp command -========================= +Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp* Syntax """""" diff --git a/doc/src/fix_nvt_sphere.rst b/doc/src/fix_nvt_sphere.rst index dd4cf9cb3f3bd63584edf34d53bcd0beddb5334d..8226328cea2a6b0f6ae66f054f8e799c5e3eb211 100644 --- a/doc/src/fix_nvt_sphere.rst +++ b/doc/src/fix_nvt_sphere.rst @@ -1,10 +1,10 @@ .. index:: fix nvt/sphere +.. index:: fix nvt/sphere/omp fix nvt/sphere command ====================== -fix nvt/sphere/omp command -========================== +Accelerator Variants: *nvt/sphere/omp* Syntax """""" diff --git a/doc/src/fix_orient.rst b/doc/src/fix_orient.rst index 51edbd48adb39f5a34aa7b6b680221c0feef5b9d..31aa6074d193c9d0dd084c97167fd20ce5d6ff64 100644 --- a/doc/src/fix_orient.rst +++ b/doc/src/fix_orient.rst @@ -1,4 +1,5 @@ .. index:: fix orient/fcc +.. index:: fix orient/bcc fix orient/fcc command ====================== diff --git a/doc/src/fix_orient_eco.rst b/doc/src/fix_orient_eco.rst index bdfab21c9d77456f804929e30b52896b4f6ba3a9..58ff38268f9e2fc25660f65cf7a83087c44ae8bb 100644 --- a/doc/src/fix_orient_eco.rst +++ b/doc/src/fix_orient_eco.rst @@ -1,4 +1,4 @@ -.. index:: fix orient/eco +.. index:: fix orient/eco fix orient/eco command ====================== diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 35749dbbfcc0f0786a72bf6b236d8141c5cdd74f..dbea88c5a977c769da5cea9d185af7ef480366f7 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -1,10 +1,10 @@ .. index:: fix property/atom +.. index:: fix property/atom/kk fix property/atom command ========================= -fix property/atom/kk command -============================ +Accelerator Variants: *property/atom/kk* Syntax """""" diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index f656049e73ef53b745a3ae655a65521e2b4ad85d..56fde059e833184333e651762619a0f43f2a16da 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -1,4 +1,8 @@ .. index:: fix qeq/point +.. index:: fix qeq/shielded +.. index:: fix qeq/slater +.. index:: fix qeq/dynamic +.. index:: fix qeq/fire fix qeq/point command ===================== diff --git a/doc/src/fix_qeq_comb.rst b/doc/src/fix_qeq_comb.rst index f70ecb1dd51d59d8f945eaad59f55392529147d3..74a97720dca1e52c7f5d8fdf9bf87ff58c54a439 100644 --- a/doc/src/fix_qeq_comb.rst +++ b/doc/src/fix_qeq_comb.rst @@ -1,10 +1,10 @@ .. index:: fix qeq/comb +.. index:: fix qeq/comb/omp fix qeq/comb command ==================== -fix qeq/comb/omp command -======================== +Accelerator Variants: *qeq/comb/omp* Syntax """""" diff --git a/doc/src/fix_qeq_reax.rst b/doc/src/fix_qeq_reax.rst index 0fd5e78578af392767204fccd57204590f7d272a..47dca86401f202a01eaba1f281a8b190c9bac1d4 100644 --- a/doc/src/fix_qeq_reax.rst +++ b/doc/src/fix_qeq_reax.rst @@ -1,13 +1,11 @@ .. index:: fix qeq/reax +.. index:: fix qeq/reax/kk +.. index:: fix qeq/reax/omp fix qeq/reax command ==================== -fix qeq/reax/kk command -======================= - -fix qeq/reax/omp command -======================== +Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp* Syntax """""" diff --git a/doc/src/fix_reaxc_bonds.rst b/doc/src/fix_reaxc_bonds.rst index 52f058192975db132c2749f925488a1c47237672..2d0d2d18db75c6cc78e4e73dbed2feb0c4f01596 100644 --- a/doc/src/fix_reaxc_bonds.rst +++ b/doc/src/fix_reaxc_bonds.rst @@ -1,10 +1,10 @@ .. index:: fix reax/c/bonds +.. index:: fix reax/c/bonds/kk fix reax/c/bonds command ======================== -fix reax/c/bonds/kk command -=========================== +Accelerator Variants: *reax/c/bonds/kk* Syntax """""" diff --git a/doc/src/fix_reaxc_species.rst b/doc/src/fix_reaxc_species.rst index 275086b52b1ac503fc9be47ba494c8ed1a94330a..9935ecaa3ac7276bd2295fece4422e09a227c643 100644 --- a/doc/src/fix_reaxc_species.rst +++ b/doc/src/fix_reaxc_species.rst @@ -1,10 +1,10 @@ .. index:: fix reax/c/species +.. index:: fix reax/c/species/kk fix reax/c/species command ========================== -fix reax/c/species/kk command -============================= +Accelerator Variants: *reax/c/species/kk* Syntax """""" diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index a14381730357cc7062e38ab29529d0cfe7ca3e0b..efadc5dd130d64d073cb89e301ee1ff61eb1077e 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -1,40 +1,49 @@ .. index:: fix rigid +.. index:: fix rigid/omp +.. index:: fix rigid/nve +.. index:: fix rigid/nve/omp +.. index:: fix rigid/nvt +.. index:: fix rigid/nvt/omp +.. index:: fix rigid/npt +.. index:: fix rigid/npt/omp +.. index:: fix rigid/nph +.. index:: fix rigid/nph/omp +.. index:: fix rigid/small +.. index:: fix rigid/small/omp +.. index:: fix rigid/nve/small +.. index:: fix rigid/nvt/small +.. index:: fix rigid/npt/small +.. index:: fix rigid/nph/small fix rigid command ================= -fix rigid/omp command -===================== +Accelerator Variants: *rigid/omp* fix rigid/nve command ===================== -fix rigid/nve/omp command -========================= +Accelerator Variants: *rigid/nve/omp* fix rigid/nvt command ===================== -fix rigid/nvt/omp command -========================= +Accelerator Variants: *rigid/nvt/omp* fix rigid/npt command ===================== -fix rigid/npt/omp command -========================= +Accelerator Variants: *rigid/npt/omp* fix rigid/nph command ===================== -fix rigid/nph/omp command -========================= +Accelerator Variants: *rigid/nph/omp* fix rigid/small command ======================= -fix rigid/small/omp command -=========================== +Accelerator Variants: *rigid/small/omp* fix rigid/nve/small command =========================== diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 7a3a95f06906498294648121d68405b58aaacf54..c1a1d0950c66ade9aef789fe9a58bc6dde34c906 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -1,10 +1,10 @@ .. index:: fix rx +.. index:: fix rx/kk fix rx command ============== -fix rx/kk command -================= +Accelerator Variants: *rx/kk* Syntax """""" diff --git a/doc/src/fix_setforce.rst b/doc/src/fix_setforce.rst index b417b369e5ad1f3282172a9359a2b488b3997990..406826e5b945562ac984865fba3c0d7002d22bfd 100644 --- a/doc/src/fix_setforce.rst +++ b/doc/src/fix_setforce.rst @@ -1,10 +1,11 @@ .. index:: fix setforce +.. index:: fix setforce/kk +.. index:: fix setforce/spin fix setforce command ==================== -fix setforce/kk command -======================= +Accelerator Variants: *setforce/kk* fix setforce/spin command ========================= diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 5f720d86ea39f5b92335a507b308fb92fd8060d1..eb7add70352d35bdfbd2c22dc3506703b44ef51d 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -1,4 +1,5 @@ .. index:: fix shake +.. index:: fix rattle fix shake command ================= diff --git a/doc/src/fix_shardlow.rst b/doc/src/fix_shardlow.rst index 3c046dae745eb98e32c24c9fad94e35465f689b5..f928044db75b6979cd8e215789288b5378daf185 100644 --- a/doc/src/fix_shardlow.rst +++ b/doc/src/fix_shardlow.rst @@ -1,10 +1,10 @@ .. index:: fix shardlow +.. index:: fix shardlow/kk fix shardlow command ==================== -fix shardlow/kk command -======================= +Accelerator Variants: *shardlow/kk* Syntax """""" diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index f7ba223965d0f2382ff5ef0c689ec094e76066c1..5b4c117452b6fb21f49c12719260f40b58b640f6 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -1,7 +1,7 @@ .. index:: fix smd/integrate_ulsph fix smd/integrate_ulsph command -================================ +=============================== Syntax """""" diff --git a/doc/src/fix_sph.rst b/doc/src/fix_sph.rst index 1b482e02520b63d669b4103872b39e92542d1e31..5ba752debb3ad90c133bdeb9cfb2f2f5e01bc39b 100644 --- a/doc/src/fix_sph.rst +++ b/doc/src/fix_sph.rst @@ -1,7 +1,7 @@ .. index:: fix sph fix sph command -================ +=============== Syntax """""" diff --git a/doc/src/fix_sph_stationary.rst b/doc/src/fix_sph_stationary.rst index 5fa3f1d04da5e73b7b8ad2336740541b2e8217b8..c86a30b542bdd8cd154c88ddf0724f8c6a0cfadc 100644 --- a/doc/src/fix_sph_stationary.rst +++ b/doc/src/fix_sph_stationary.rst @@ -1,7 +1,7 @@ .. index:: fix sph/stationary fix sph/stationary command -=========================== +========================== Syntax """""" diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 10c92dc2f233c28a1b4bb5b9e135542d9af7de62..8faa6035cf2583704a7a073bccd1a666f283fc98 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -1,4 +1,5 @@ .. index:: fix temp/csvr +.. index:: fix temp/csld fix temp/csvr command ===================== diff --git a/doc/src/fix_ttm.rst b/doc/src/fix_ttm.rst index 97cb0cd05ba54e35a3eab8b01ace2e66404393c0..24bc6f297f9847af5280e9373983233812e5900e 100644 --- a/doc/src/fix_ttm.rst +++ b/doc/src/fix_ttm.rst @@ -1,4 +1,5 @@ .. index:: fix ttm +.. index:: fix ttm/mod fix ttm command =============== diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index d4120ca625d887e715f46380a2f3b3b4b8624fe5..39ff8791382889fb6fe1d52211f08a5751189e8c 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -1,10 +1,15 @@ .. index:: fix wall/lj93 +.. index:: fix wall/lj93/kk +.. index:: fix wall/lj126 +.. index:: fix wall/lj1043 +.. index:: fix wall/colloid +.. index:: fix wall/harmonic +.. index:: fix wall/morse fix wall/lj93 command ===================== -fix wall/lj93/kk command -======================== +Accelerator Variants: *wall/lj93/kk* fix wall/lj126 command ====================== diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index 79f96765f8b5a89ecfcd7e1f031d44e480b2a8d9..2bab8c60560e06e62147d24916183f7b51c12a05 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -1,4 +1,5 @@ .. index:: fix wall/ees +.. index:: fix wall/region/ees fix wall/ees command ==================== diff --git a/doc/src/fix_wall_reflect.rst b/doc/src/fix_wall_reflect.rst index 44cde8f3d5b5237e519065cdaa282a2e42fc8055..4f014cc628d105535debc8173c442493aa37abe0 100644 --- a/doc/src/fix_wall_reflect.rst +++ b/doc/src/fix_wall_reflect.rst @@ -1,10 +1,10 @@ .. index:: fix wall/reflect +.. index:: fix wall/reflect/kk fix wall/reflect command ======================== -fix wall/reflect/kk command -=========================== +Accelerator Variants: *wall/reflect/kk* Syntax """""" diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index eb6b8eab2cf8ea3c4b7e76dd8eeb5416f07ac2cd..a84e92b090114b4e94c758d14f5406903fa2d85e 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -1,13 +1,11 @@ .. index:: improper_style class2 +.. index:: improper_style class2/omp +.. index:: improper_style class2/kk improper_style class2 command ============================= -improper_style class2/omp command -================================= - -improper_style class2/kk command -================================ +Accelerator Variants: *class2/omp*, *class2/kk* Syntax """""" diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index 70885acc284e0c7d9811daaa69450ccbe095c2fa..a6281bc26010169f52cfcb3dd67f19a2a8b98a84 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -1,10 +1,10 @@ .. index:: improper_style cossq +.. index:: improper_style cossq/omp improper_style cossq command ============================ -improper_style cossq/omp command -================================ +Accelerator Variants: *cossq/omp* Syntax """""" diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index bde510c3f7d5748eb0dda6c7d6284cab2602194b..5bd7fdf911ce9f458b303442381b60f457b1f5e4 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -1,13 +1,11 @@ .. index:: improper_style cvff +.. index:: improper_style cvff/intel +.. index:: improper_style cvff/omp improper_style cvff command =========================== -improper_style cvff/intel command -================================= - -improper_style cvff/omp command -=============================== +Accelerator Variants: *cvff/intel*, *cvff/omp* Syntax """""" diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 04ce9ba994d36a6dd2ade221bea559ebb546f7ac..84ea97509dd3b1c4028c439ffa793312174c45a1 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -1,10 +1,10 @@ .. index:: improper_style fourier +.. index:: improper_style fourier/omp improper_style fourier command ============================== -improper_style fourier/omp command -================================== +Accelerator Variants: *fourier/omp* Syntax """""" diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index e1b78d21dba2d069c977530de7da2bbac7ecc2df..4f21e48fa9ad036431ab70259e7701cba21edbde 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -1,16 +1,12 @@ .. index:: improper_style harmonic +.. index:: improper_style harmonic/intel +.. index:: improper_style harmonic/kk +.. index:: improper_style harmonic/omp improper_style harmonic command =============================== -improper_style harmonic/intel command -===================================== - -improper_style harmonic/kk command -================================== - -improper_style harmonic/omp command -=================================== +Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp* Syntax """""" diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index df319396e21d6b30c515d1116567d017d35f8ad7..d67c999714a5724322972dcfa5fff155ede2e676 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -1,10 +1,10 @@ .. index:: improper_style ring +.. index:: improper_style ring/omp improper_style ring command =========================== -improper_style ring/omp command -=============================== +Accelerator Variants: *ring/omp* Syntax """""" diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 10981248d9fd0f30a27b85f2dd5d35b2ffb1b734..5d4aa571e185c6ec11ae3753d2fd11cbfde9f822 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -1,10 +1,10 @@ .. index:: improper_style umbrella +.. index:: improper_style umbrella/omp improper_style umbrella command =============================== -improper_style umbrella/omp command -=================================== +Accelerator Variants: *umbrella/omp* Syntax """""" diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 5b45b00353e6f7bd7111d8c10bd8f212d12183bb..59f5b7f27c419b4249220e992680815ae863884b 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -1,4 +1,30 @@ -.. index:: kspace_style +.. index:: kspace_style ewald +.. index:: kspace_style ewald/dipole +.. index:: kspace_style ewald/dipole/spin +.. index:: kspace_style ewald/disp +.. index:: kspace_style ewald/omp +.. index:: kspace_style pppm +.. index:: kspace_style pppm/kk +.. index:: kspace_style pppm/omp +.. index:: kspace_style pppm/gpu +.. index:: kspace_style pppm/intel +.. index:: kspace_style pppm/cg +.. index:: kspace_style pppm/dipole +.. index:: kspace_style pppm/dipole/spin +.. index:: kspace_style pppm/disp +.. index:: kspace_style pppm/disp/omp +.. index:: kspace_style pppm/disp/tip4p +.. index:: kspace_style pppm/disp/tip4p/omp +.. index:: kspace_style pppm/disp/intel +.. index:: kspace_style pppm/cg/omp +.. index:: kspace_style pppm/stagger +.. index:: kspace_style pppm/tip4p +.. index:: kspace_style pppm/tip4p/omp +.. index:: kspace_style msm +.. index:: kspace_style msm/omp +.. index:: kspace_style msm/cg +.. index:: kspace_style msm/cg/omp +.. index:: kspace_style scafacos kspace_style command ==================== diff --git a/doc/src/pair_adp.rst b/doc/src/pair_adp.rst index 70175499252eb4035af2ab70f4a1dba9c9de6bbf..5eec0004bf04350a55a3b82947290bd084c1ce88 100644 --- a/doc/src/pair_adp.rst +++ b/doc/src/pair_adp.rst @@ -1,10 +1,10 @@ .. index:: pair_style adp +.. index:: pair_style adp/omp pair_style adp command ====================== -pair_style adp/omp command -========================== +Accelerator Variants: *adp/omp* Syntax """""" diff --git a/doc/src/pair_agni.rst b/doc/src/pair_agni.rst index ee69f40d8043ccb9e143298e03845d1f6ffbd3d6..087c39e8f9bba3ff802f6b3bd697f7d525730a2a 100644 --- a/doc/src/pair_agni.rst +++ b/doc/src/pair_agni.rst @@ -1,10 +1,10 @@ .. index:: pair_style agni +.. index:: pair_style agni/omp pair_style agni command -======================== +======================= -pair_style agni/omp command -============================ +Accelerator Variants: *agni/omp* Syntax """""" diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index f3be0e85de35131843965b403ae0753a4860b646..d631d0a3d0692f7a5a3c483a43887508881f5546 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -1,31 +1,27 @@ .. index:: pair_style airebo +.. index:: pair_style airebo/intel +.. index:: pair_style airebo/omp +.. index:: pair_style airebo/morse +.. index:: pair_style airebo/morse/intel +.. index:: pair_style airebo/morse/omp +.. index:: pair_style rebo +.. index:: pair_style rebo/intel +.. index:: pair_style rebo/omp pair_style airebo command ========================= -pair_style airebo/intel command -=============================== - -pair_style airebo/omp command -============================= +Accelerator Variants: *airebo/intel*, *airebo/omp* pair_style airebo/morse command =============================== -pair_style airebo/morse/intel command -===================================== - -pair_style airebo/morse/omp command -=================================== +Accelerator Variants: *airebo/morse/intel*, *airebo/morse/omp* pair_style rebo command ======================= -pair_style rebo/intel command -============================= - -pair_style rebo/omp command -=========================== +Accelerator Variants: *rebo/intel*, *rebo/omp* Syntax """""" diff --git a/doc/src/pair_beck.rst b/doc/src/pair_beck.rst index 0e63fe77ba1806d9ac65db448bb08f0ffb2c7afd..44bc317138b4ac00d606b932390657c44977147d 100644 --- a/doc/src/pair_beck.rst +++ b/doc/src/pair_beck.rst @@ -1,13 +1,11 @@ .. index:: pair_style beck +.. index:: pair_style beck/gpu +.. index:: pair_style beck/omp pair_style beck command ======================= -pair_style beck/gpu command -=========================== - -pair_style beck/omp command -=========================== +Accelerator Variants: *beck/gpu*, *beck/omp* Syntax """""" diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index 761b40b81291eb370143b84839fbf582904003bf..65be948f82559da4f6b003d0c0c31170f6d8b316 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -1,37 +1,35 @@ .. index:: pair_style born +.. index:: pair_style born/omp +.. index:: pair_style born/gpu +.. index:: pair_style born/coul/long +.. index:: pair_style born/coul/long/gpu +.. index:: pair_style born/coul/long/omp +.. index:: pair_style born/coul/msm +.. index:: pair_style born/coul/msm/omp +.. index:: pair_style born/coul/wolf +.. index:: pair_style born/coul/wolf/gpu +.. index:: pair_style born/coul/wolf/omp +.. index:: pair_style born/coul/dsf pair_style born command ======================= -pair_style born/omp command -=========================== - -pair_style born/gpu command -=========================== +Accelerator Variants: *born/omp*, *born/gpu* pair_style born/coul/long command ================================= -pair_style born/coul/long/gpu command -===================================== - -pair_style born/coul/long/omp command -===================================== +Accelerator Variants: *born/coul/long/gpu*, *born/coul/long/omp* pair_style born/coul/msm command ================================ -pair_style born/coul/msm/omp command -==================================== +Accelerator Variants: *born/coul/msm/omp* pair_style born/coul/wolf command ================================= -pair_style born/coul/wolf/gpu command -===================================== - -pair_style born/coul/wolf/omp command -===================================== +Accelerator Variants: *born/coul/wolf/gpu*, *born/coul/wolf/omp* pair_style born/coul/dsf command ================================ diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index ea311d603e1c44ae845848d50d78ac42db7df2d0..43c17c9087520a6c84ff404c0f3246f376a4bd5b 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -1,16 +1,17 @@ .. index:: pair_style brownian +.. index:: pair_style brownian/omp +.. index:: pair_style brownian/poly +.. index:: pair_style brownian/poly/omp pair_style brownian command =========================== -pair_style brownian/omp command -================================ +Accelerator Variants: *brownian/omp* pair_style brownian/poly command ================================ -pair_style brownian/poly/omp command -==================================== +Accelerator Variants: *brownian/poly/omp* Syntax """""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index e8a1475ccb5aa31f77c288b280c0b23f5b7adc79..5f255ece3907aa66f031afdcb7bdcc9ea480c001 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -1,55 +1,40 @@ .. index:: pair_style buck +.. index:: pair_style buck/gpu +.. index:: pair_style buck/intel +.. index:: pair_style buck/kk +.. index:: pair_style buck/omp +.. index:: pair_style buck/coul/cut +.. index:: pair_style buck/coul/cut/gpu +.. index:: pair_style buck/coul/cut/intel +.. index:: pair_style buck/coul/cut/kk +.. index:: pair_style buck/coul/cut/omp +.. index:: pair_style buck/coul/long +.. index:: pair_style buck/coul/long/gpu +.. index:: pair_style buck/coul/long/intel +.. index:: pair_style buck/coul/long/kk +.. index:: pair_style buck/coul/long/omp +.. index:: pair_style buck/coul/msm +.. index:: pair_style buck/coul/msm/omp pair_style buck command -======================== +======================= -pair_style buck/gpu command -============================ - -pair_style buck/intel command -============================== - -pair_style buck/kk command -=========================== - -pair_style buck/omp command -============================ +Accelerator Variants: *buck/gpu*, *buck/intel*, *buck/kk*, *buck/omp* pair_style buck/coul/cut command -================================= - -pair_style buck/coul/cut/gpu command -===================================== - -pair_style buck/coul/cut/intel command -======================================= +================================ -pair_style buck/coul/cut/kk command -==================================== - -pair_style buck/coul/cut/omp command -===================================== +Accelerator Variants: *buck/coul/cut/gpu*, *buck/coul/cut/intel*, *buck/coul/cut/kk*, *buck/coul/cut/omp* pair_style buck/coul/long command -================================== - -pair_style buck/coul/long/gpu command -====================================== - -pair_style buck/coul/long/intel command -======================================== - -pair_style buck/coul/long/kk command -===================================== +================================= -pair_style buck/coul/long/omp command -====================================== +Accelerator Variants: *buck/coul/long/gpu*, *buck/coul/long/intel*, *buck/coul/long/kk*, *buck/coul/long/omp* pair_style buck/coul/msm command -================================= +================================ -pair_style buck/coul/msm/omp command -===================================== +Accelerator Variants: *buck/coul/msm/omp* Syntax """""" diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 7d3e5b9a22f1d5cd3b731b1b43612da003365c42..5f96a93fee314aaa5a5c8cedc3137e9a40f6dbf3 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -1,4 +1,5 @@ .. index:: pair_style buck6d/coul/gauss/dsf +.. index:: pair_style buck6d/coul/gauss/long pair_style buck6d/coul/gauss/dsf command ======================================== diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index c0dd81d78fb90e86a34168732a74d90747cf51d3..1883cee637be4736ad96b362f57c59e5babe051a 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -1,10 +1,10 @@ .. index:: pair_style buck/long/coul/long +.. index:: pair_style buck/long/coul/long/omp pair_style buck/long/coul/long command -======================================= +====================================== -pair_style buck/long/coul/long/omp command -=========================================== +Accelerator Variants: *buck/long/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index 183311e34d4a73be3aafcb943c799a41b64c4038..6d81266a35ac0fa0c5f431bc0421825b478ac24e 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -1,55 +1,46 @@ .. index:: pair_style lj/charmm/coul/charmm +.. index:: pair_style lj/charmm/coul/charmm/intel +.. index:: pair_style lj/charmm/coul/charmm/kk +.. index:: pair_style lj/charmm/coul/charmm/omp +.. index:: pair_style lj/charmm/coul/charmm/implicit +.. index:: pair_style lj/charmm/coul/charmm/implicit/kk +.. index:: pair_style lj/charmm/coul/charmm/implicit/omp +.. index:: pair_style lj/charmm/coul/long +.. index:: pair_style lj/charmm/coul/long/gpu +.. index:: pair_style lj/charmm/coul/long/intel +.. index:: pair_style lj/charmm/coul/long/kk +.. index:: pair_style lj/charmm/coul/long/opt +.. index:: pair_style lj/charmm/coul/long/omp +.. index:: pair_style lj/charmm/coul/msm +.. index:: pair_style lj/charmm/coul/msm/omp +.. index:: pair_style lj/charmmfsw/coul/charmmfsh +.. index:: pair_style lj/charmmfsw/coul/long pair_style lj/charmm/coul/charmm command -========================================= - -pair_style lj/charmm/coul/charmm/intel command -=============================================== - -pair_style lj/charmm/coul/charmm/kk command -============================================ +======================================== -pair_style lj/charmm/coul/charmm/omp command -============================================= +Accelerator Variants: *lj/charmm/coul/charmm/intel*, *lj/charmm/coul/charmm/kk*, *lj/charmm/coul/charmm/omp* pair_style lj/charmm/coul/charmm/implicit command -================================================== +================================================= -pair_style lj/charmm/coul/charmm/implicit/kk command -===================================================== - -pair_style lj/charmm/coul/charmm/implicit/omp command -====================================================== +Accelerator Variants: *lj/charmm/coul/charmm/implicit/kk*, *lj/charmm/coul/charmm/implicit/omp* pair_style lj/charmm/coul/long command -======================================= - -pair_style lj/charmm/coul/long/gpu command -=========================================== - -pair_style lj/charmm/coul/long/intel command -============================================= - -pair_style lj/charmm/coul/long/kk command -========================================== - -pair_style lj/charmm/coul/long/opt command -=========================================== +====================================== -pair_style lj/charmm/coul/long/omp command -=========================================== +Accelerator Variants: *lj/charmm/coul/long/gpu*, *lj/charmm/coul/long/intel*, *lj/charmm/coul/long/kk*, *lj/charmm/coul/long/opt*, *lj/charmm/coul/long/omp* pair_style lj/charmm/coul/msm command -====================================== +===================================== -pair_style lj/charmm/coul/msm/omp command -========================================== +Accelerator Variants: *lj/charmm/coul/msm/omp* pair_style lj/charmmfsw/coul/charmmfsh command -=============================================== +============================================== pair_style lj/charmmfsw/coul/long command -========================================== +========================================= Syntax """""" diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index 66a696938f1044df379fd757635ee2df0152c291..cfa085cc28024a2eb4aa2603e247e0e34e718b9f 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -1,37 +1,29 @@ .. index:: pair_style lj/class2 +.. index:: pair_style lj/class2/gpu +.. index:: pair_style lj/class2/kk +.. index:: pair_style lj/class2/omp +.. index:: pair_style lj/class2/coul/cut +.. index:: pair_style lj/class2/coul/cut/kk +.. index:: pair_style lj/class2/coul/cut/omp +.. index:: pair_style lj/class2/coul/long +.. index:: pair_style lj/class2/coul/long/gpu +.. index:: pair_style lj/class2/coul/long/kk +.. index:: pair_style lj/class2/coul/long/omp pair_style lj/class2 command ============================ -pair_style lj/class2/gpu command -================================ - -pair_style lj/class2/kk command -=============================== - -pair_style lj/class2/omp command -================================ +Accelerator Variants: *lj/class2/gpu*, *lj/class2/kk*, *lj/class2/omp* pair_style lj/class2/coul/cut command ===================================== -pair_style lj/class2/coul/cut/kk command -======================================== - -pair_style lj/class2/coul/cut/omp command -========================================= +Accelerator Variants: *lj/class2/coul/cut/kk*, *lj/class2/coul/cut/omp* pair_style lj/class2/coul/long command ====================================== -pair_style lj/class2/coul/long/gpu command -========================================== - -pair_style lj/class2/coul/long/kk command -========================================= - -pair_style lj/class2/coul/long/omp command -========================================== +Accelerator Variants: *lj/class2/coul/long/gpu*, *lj/class2/coul/long/kk*, *lj/class2/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 4bb82e961571463e90baf3dc90d4033dd8936f55..040bea248711d7e06d04fe89302a054a65ebde09 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -1,13 +1,11 @@ .. index:: pair_style colloid +.. index:: pair_style colloid/gpu +.. index:: pair_style colloid/omp pair_style colloid command ========================== -pair_style colloid/gpu command -============================== - -pair_style colloid/omp command -============================== +Accelerator Variants: *colloid/gpu*, *colloid/omp* Syntax """""" diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 441f982996313e4810ba82a8aec502719e2f23c6..2e164d46fcd2a75f61f1076a7742409f6fd5f91f 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -1,10 +1,11 @@ .. index:: pair_style comb +.. index:: pair_style comb/omp +.. index:: pair_style comb3 pair_style comb command ======================= -pair_style comb/omp command -=========================== +Accelerator Variants: *comb/omp* pair_style comb3 command ======================== diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index 4874bf044e8f8c840866324901aef3f6b1890ab5..4def43647f7e0aa5e06b7a2314eb90cf77259edf 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -1,58 +1,54 @@ .. index:: pair_style coul/cut +.. index:: pair_style coul/cut/gpu +.. index:: pair_style coul/cut/kk +.. index:: pair_style coul/cut/omp +.. index:: pair_style coul/debye +.. index:: pair_style coul/debye/gpu +.. index:: pair_style coul/debye/kk +.. index:: pair_style coul/debye/omp +.. index:: pair_style coul/dsf +.. index:: pair_style coul/dsf/gpu +.. index:: pair_style coul/dsf/kk +.. index:: pair_style coul/dsf/omp +.. index:: pair_style coul/long +.. index:: pair_style coul/long/omp +.. index:: pair_style coul/long/kk +.. index:: pair_style coul/long/gpu +.. index:: pair_style coul/msm +.. index:: pair_style coul/msm/omp +.. index:: pair_style coul/streitz +.. index:: pair_style coul/wolf +.. index:: pair_style coul/wolf/kk +.. index:: pair_style coul/wolf/omp +.. index:: pair_style tip4p/cut +.. index:: pair_style tip4p/cut/omp +.. index:: pair_style tip4p/long +.. index:: pair_style tip4p/long/omp pair_style coul/cut command =========================== -pair_style coul/cut/gpu command -=============================== - -pair_style coul/cut/kk command -============================== - -pair_style coul/cut/omp command -=============================== +Accelerator Variants: *coul/cut/gpu*, *coul/cut/kk*, *coul/cut/omp* pair_style coul/debye command ============================= -pair_style coul/debye/gpu command -================================= - -pair_style coul/debye/kk command -================================ - -pair_style coul/debye/omp command -================================= +Accelerator Variants: *coul/debye/gpu*, *coul/debye/kk*, *coul/debye/omp* pair_style coul/dsf command =========================== -pair_style coul/dsf/gpu command -=============================== - -pair_style coul/dsf/kk command -============================== - -pair_style coul/dsf/omp command -=============================== +Accelerator Variants: *coul/dsf/gpu*, *coul/dsf/kk*, *coul/dsf/omp* pair_style coul/long command ============================ -pair_style coul/long/omp command -================================ - -pair_style coul/long/gpu command -================================ - -pair_style coul/long/kk command -=============================== +Accelerator Variants: *coul/long/omp*, *coul/long/kk*, *coul/long/gpu* pair_style coul/msm command =========================== -pair_style coul/msm/omp command -=============================== +Accelerator Variants: *coul/msm/omp* pair_style coul/streitz command =============================== @@ -60,23 +56,17 @@ pair_style coul/streitz command pair_style coul/wolf command ============================ -pair_style coul/wolf/kk command -=============================== - -pair_style coul/wolf/omp command -================================ +Accelerator Variants: *coul/wolf/kk*, *coul/wolf/omp* pair_style tip4p/cut command ============================ +Accelerator Variants: *tip4p/cut/omp* + pair_style tip4p/long command ============================= -pair_style tip4p/cut/omp command -================================ - -pair_style tip4p/long/omp command -================================= +Accelerator Variants: *tip4p/long/omp* Syntax """""" diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index e979ceef3176cd55956e8279602a550104e330df..bcf0c48e4d882c2776cb1ed6935d3552570b44d3 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -1,10 +1,10 @@ .. index:: pair_style coul/diel +.. index:: pair_style coul/diel/omp pair_style coul/diel command ============================ -pair_style coul/diel/omp command -================================ +Accelerator Variants: *coul/diel/omp* Syntax """""" diff --git a/doc/src/pair_coul_slater.rst b/doc/src/pair_coul_slater.rst index cc8e6f243c5c112e33cfbf258169fe00be03d237..a4d8b253b1c2aa3d473050a2bc390a9194d5918c 100644 --- a/doc/src/pair_coul_slater.rst +++ b/doc/src/pair_coul_slater.rst @@ -1,4 +1,9 @@ .. index:: pair_style coul/slater +.. index:: pair_style coul/slater/cut +.. index:: pair_style coul/slater/long + +pair_style coul/slater command +============================== pair_style coul/slater/cut command ================================== diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 8efd49197d792bb4110c8d8a3dffceb1b9a28767..f41d8402166fde4ce6a862cd45d9e802b08f7fc5 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -1,37 +1,44 @@ .. index:: pair_style born/coul/dsf/cs +.. index:: pair_style born/coul/long/cs +.. index:: pair_style born/coul/long/cs/gpu +.. index:: pair_style born/coul/wolf/cs +.. index:: pair_style born/coul/wolf/cs/gpu +.. index:: pair_style buck/coul/long/cs +.. index:: pair_style coul/long/cs +.. index:: pair_style coul/long/cs/gpu +.. index:: pair_style coul/wolf/cs +.. index:: pair_style lj/cut/coul/long/cs +.. index:: pair_style lj/class2/coul/long/cs pair_style born/coul/dsf/cs command -==================================== +=================================== pair_style born/coul/long/cs command -===================================== +==================================== -pair_style born/coul/long/cs/gpu command -========================================= +Accelerator Variants: *born/coul/long/cs/gpu* pair_style born/coul/wolf/cs command -===================================== +==================================== -pair_style born/coul/wolf/cs/gpu command -========================================= +Accelerator Variants: *born/coul/wolf/cs/gpu* pair_style buck/coul/long/cs command -===================================== +==================================== pair_style coul/long/cs command -================================ +=============================== -pair_style coul/long/cs/gpu command -==================================== +Accelerator Variants: *coul/long/cs/gpu* pair_style coul/wolf/cs command -================================ +=============================== pair_style lj/cut/coul/long/cs command -======================================= +====================================== pair_style lj/class2/coul/long/cs command -========================================== +========================================= Syntax """""" diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 21548be4f0d433085825b0cca4a8ecdb93806abd..602c374d9f96a4a959b186f363342f41d9f165a0 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -1,28 +1,27 @@ .. index:: pair_style lj/cut/dipole/cut +.. index:: pair_style lj/cut/dipole/cut/gpu +.. index:: pair_style lj/cut/dipole/cut/omp +.. index:: pair_style lj/sf/dipole/sf +.. index:: pair_style lj/sf/dipole/sf/gpu +.. index:: pair_style lj/sf/dipole/sf/omp +.. index:: pair_style lj/cut/dipole/long +.. index:: pair_style lj/cut/dipole/long/gpu +.. index:: pair_style lj/long/dipole/long pair_style lj/cut/dipole/cut command ==================================== -pair_style lj/cut/dipole/cut/gpu command -======================================== - -pair_style lj/cut/dipole/cut/omp command -======================================== +Accelerator Variants: *lj/cut/dipole/cut/gpu*, *lj/cut/dipole/cut/omp* pair_style lj/sf/dipole/sf command ================================== -pair_style lj/sf/dipole/sf/gpu command -====================================== - -pair_style lj/sf/dipole/sf/omp command -====================================== +Accelerator Variants: *lj/sf/dipole/sf/gpu*, *lj/sf/dipole/sf/omp* pair_style lj/cut/dipole/long command ===================================== -pair_style lj/cut/dipole/long/gpu command -========================================= +Accelerator Variants: *lj/cut/dipole/long/gpu* pair_style lj/long/dipole/long command ====================================== diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 94c9fa9bea55899cbb8ddc4af9204fe8dbfd747e..d1d84407c443d46e0c33286448c4584ad07df141 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -1,25 +1,20 @@ .. index:: pair_style dpd +.. index:: pair_style dpd/gpu +.. index:: pair_style dpd/intel +.. index:: pair_style dpd/omp +.. index:: pair_style dpd/tstat +.. index:: pair_style dpd/tstat/gpu +.. index:: pair_style dpd/tstat/omp pair_style dpd command ====================== -pair_style dpd/gpu command -========================== - -pair_style dpd/intel command -============================ - -pair_style dpd/omp command -========================== +Accelerator Variants: *dpd/gpu*, *dpd/intel*, *dpd/omp* pair_style dpd/tstat command ============================ -pair_style dpd/tstat/gpu command -================================ - -pair_style dpd/tstat/omp command -================================ +Accelerator Variants: *dpd/tstat/gpu*, *dpd/tstat/omp* Syntax """""" diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index e0659a7b789f5899425f0238c4315c5a564948bb..bb810b0fe6dd8755559febb6ca35741eab56fb88 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -1,4 +1,6 @@ .. index:: pair_style dpd/fdt +.. index:: pair_style dpd/fdt/energy +.. index:: pair_style dpd/fdt/energy/kk pair_style dpd/fdt command ========================== @@ -6,8 +8,7 @@ pair_style dpd/fdt command pair_style dpd/fdt/energy command ================================= -pair_style dpd/fdt/energy/kk command -==================================== +Accelerator Variants: *dpd/fdt/energy/kk* Syntax """""" diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index c5f9b26435bae1ef81b67970d2e869dba2602bef..690b387bad4af2b99bb53fd5912be1b1ca6cfff0 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -1,40 +1,33 @@ .. index:: pair_style eam +.. index:: pair_style eam/gpu +.. index:: pair_style eam/intel +.. index:: pair_style eam/kk +.. index:: pair_style eam/omp +.. index:: pair_style eam/opt +.. index:: pair_style eam/alloy +.. index:: pair_style eam/alloy/gpu +.. index:: pair_style eam/alloy/intel +.. index:: pair_style eam/alloy/kk +.. index:: pair_style eam/alloy/omp +.. index:: pair_style eam/alloy/opt +.. index:: pair_style eam/cd +.. index:: pair_style eam/cd/old +.. index:: pair_style eam/fs +.. index:: pair_style eam/fs/gpu +.. index:: pair_style eam/fs/intel +.. index:: pair_style eam/fs/kk +.. index:: pair_style eam/fs/omp +.. index:: pair_style eam/fs/opt pair_style eam command ====================== -pair_style eam/gpu command -========================== - -pair_style eam/intel command -============================ - -pair_style eam/kk command -========================= - -pair_style eam/omp command -========================== - -pair_style eam/opt command -========================== +Accelerator Variants: *eam/gpu*, *eam/intel*, *eam/kk*, *eam/omp*, *eam/opt* pair_style eam/alloy command ============================ -pair_style eam/alloy/gpu command -================================ - -pair_style eam/alloy/intel command -================================== - -pair_style eam/alloy/kk command -=============================== - -pair_style eam/alloy/omp command -================================ - -pair_style eam/alloy/opt command -================================ +Accelerator Variants: *eam/alloy/gpu*, *eam/alloy/intel*, *eam/alloy/kk*, *eam/alloy/omp*, *eam/alloy/opt* pair_style eam/cd command ========================= @@ -45,20 +38,7 @@ pair_style eam/cd/old command pair_style eam/fs command ========================= -pair_style eam/fs/gpu command -============================= - -pair_style eam/fs/intel command -=============================== - -pair_style eam/fs/kk command -============================ - -pair_style eam/fs/omp command -============================= - -pair_style eam/fs/opt command -============================= +Accelerator Variants: *eam/fs/gpu*, *eam/fs/intel*, *eam/fs/kk*, *eam/fs/omp*, *eam/fs/opt* Syntax """""" diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index d8e747ddf4fa0a18662ddab4f9a2d0e316b0d9e0..8f8d70f2f604b74221f5201a4f056e56b6848c0c 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -1,10 +1,11 @@ .. index:: pair_style edip +.. index:: pair_style edip/omp +.. index:: pair_style edip/multi pair_style edip command ======================= -pair_style edip/omp command -=========================== +Accelerator Variants: *edip/omp* pair_style edip/multi command ============================= diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index aef7dba3a4a8315629856aecf81f69810a45c73a..8360dbab64e92a906719f5268a97dce3fc640fb7 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -1,10 +1,10 @@ .. index:: pair_style eim +.. index:: pair_style eim/omp pair_style eim command ====================== -pair_style eim/omp command -========================== +Accelerator Variants: *eim/omp* Syntax """""" diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index d6fe4850ced84ad30d2165aa5bdd0c78f71132e0..49a4c5436fc1303aac17726b8d009549ca154be3 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style exp6/rx +.. index:: pair_style exp6/rx/kk pair_style exp6/rx command ========================== -pair_style exp6/rx/kk command -============================= +Accelerator Variants: *exp6/rx/kk* Syntax """""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index bd38fe1ec950c43428cae151e4c29f9b06219108..109ddfdf21c2545c5bb9d4e6011d63bfe13ab5d0 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -1,64 +1,75 @@ .. index:: pair_style lj/cut/soft +.. index:: pair_style lj/cut/soft/omp +.. index:: pair_style lj/cut/coul/cut/soft +.. index:: pair_style lj/cut/coul/cut/soft/omp +.. index:: pair_style lj/cut/coul/long/soft +.. index:: pair_style lj/cut/coul/long/soft/omp +.. index:: pair_style lj/cut/tip4p/long/soft +.. index:: pair_style lj/cut/tip4p/long/soft/omp +.. index:: pair_style lj/charmm/coul/long/soft +.. index:: pair_style lj/charmm/coul/long/soft/omp +.. index:: pair_style lj/class2/soft +.. index:: pair_style lj/class2/coul/cut/soft +.. index:: pair_style lj/class2/coul/long/soft +.. index:: pair_style coul/cut/soft +.. index:: pair_style coul/cut/soft/omp +.. index:: pair_style coul/long/soft +.. index:: pair_style coul/long/soft/omp +.. index:: pair_style tip4p/long/soft +.. index:: pair_style tip4p/long/soft/omp +.. index:: pair_style morse/soft pair_style lj/cut/soft command ============================== -pair_style lj/cut/soft/omp command -================================== +Accelerator Variants: *lj/cut/soft/omp* pair_style lj/cut/coul/cut/soft command ======================================= -pair_style lj/cut/coul/cut/soft/omp command -=========================================== +Accelerator Variants: *lj/cut/coul/cut/soft/omp* pair_style lj/cut/coul/long/soft command ======================================== -pair_style lj/cut/coul/long/soft/omp command -============================================ +Accelerator Variants: *lj/cut/coul/long/soft/omp* pair_style lj/cut/tip4p/long/soft command -========================================== +========================================= -pair_style lj/cut/tip4p/long/soft/omp command -============================================== +Accelerator Variants: *lj/cut/tip4p/long/soft/omp* pair_style lj/charmm/coul/long/soft command -============================================ +=========================================== -pair_style lj/charmm/coul/long/soft/omp command -================================================ +Accelerator Variants: *lj/charmm/coul/long/soft/omp* pair_style lj/class2/soft command -================================== +================================= pair_style lj/class2/coul/cut/soft command -=========================================== +========================================== pair_style lj/class2/coul/long/soft command -============================================ +=========================================== pair_style coul/cut/soft command -================================= +================================ -pair_style coul/cut/soft/omp command -===================================== +Accelerator Variants: *coul/cut/soft/omp* pair_style coul/long/soft command -================================== +================================= -pair_style coul/long/soft/omp command -====================================== +Accelerator Variants: *coul/long/soft/omp* pair_style tip4p/long/soft command -=================================== +================================== -pair_style tip4p/long/soft/omp command -======================================= +Accelerator Variants: *tip4p/long/soft/omp* pair_style morse/soft command -============================== +============================= Syntax """""" diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 8c7ce7417490ff7815b3e7e77dcb4f1c7804a776..9b516cce7bf7fcfd5ec57de27520458a35c85f83 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -1,19 +1,18 @@ .. index:: pair_style gauss +.. index:: pair_style gauss/gpu +.. index:: pair_style gauss/omp +.. index:: pair_style gauss/cut +.. index:: pair_style gauss/cut/omp pair_style gauss command ======================== -pair_style gauss/gpu command -============================ - -pair_style gauss/omp command -============================ +Accelerator Variants: *gauss/gpu*, *gauss/omp* pair_style gauss/cut command ============================ -pair_style gauss/cut/omp command -================================ +Accelerator Variants: *gauss/cut/omp* Syntax """""" diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index 1e8094feeff331a785eda88657472bbc8e03bf29..309e949f97184d0f9d42e811ff4b7fe38c250c0d 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -1,16 +1,12 @@ .. index:: pair_style gayberne +.. index:: pair_style gayberne/gpu +.. index:: pair_style gayberne/intel +.. index:: pair_style gayberne/omp pair_style gayberne command =========================== -pair_style gayberne/gpu command -=============================== - -pair_style gayberne/intel command -================================= - -pair_style gayberne/omp command -=============================== +Accelerator Variants: *gayberne/gpu*, *gayberne/intel*, *gayberne/omp* Syntax """""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 9aacfdfa315043b8b468e6a70fb30690acc67e59..d3f87839e87ee0679cdc97b1f3a00bd48806c087 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -1,25 +1,25 @@ .. index:: pair_style gran/hooke +.. index:: pair_style gran/hooke/omp +.. index:: pair_style gran/hooke/history +.. index:: pair_style gran/hooke/history/omp +.. index:: pair_style gran/hooke/history/kk +.. index:: pair_style gran/hertz/history +.. index:: pair_style gran/hertz/history/omp pair_style gran/hooke command ============================= -pair_style gran/hooke/omp command -================================= +Accelerator Variants: *gran/hooke/omp* pair_style gran/hooke/history command ===================================== -pair_style gran/hooke/history/omp command -========================================= - -pair_style gran/hooke/history/kk command -======================================== +Accelerator Variants: *gran/hooke/history/omp*, *gran/hooke/history/kk* pair_style gran/hertz/history command ===================================== -pair_style gran/hertz/history/omp command -========================================= +Accelerator Variants: *gran/hertz/history/omp* Syntax """""" diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index a4c065e24dc90d4b047574732d60d94eaaca48c9..88cb4ce880e31ae6b8323dd94787ca87a2836d27 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -1,25 +1,20 @@ .. index:: pair_style lj/gromacs +.. index:: pair_style lj/gromacs/gpu +.. index:: pair_style lj/gromacs/kk +.. index:: pair_style lj/gromacs/omp +.. index:: pair_style lj/gromacs/coul/gromacs +.. index:: pair_style lj/gromacs/coul/gromacs/kk +.. index:: pair_style lj/gromacs/coul/gromacs/omp pair_style lj/gromacs command ============================= -pair_style lj/gromacs/gpu command -================================= - -pair_style lj/gromacs/kk command -================================ - -pair_style lj/gromacs/omp command -================================= +Accelerator Variants: *lj/gromacs/gpu*, *lj/gromacs/kk*, *lj/gromacs/omp* pair_style lj/gromacs/coul/gromacs command ========================================== -pair_style lj/gromacs/coul/gromacs/kk command -============================================= - -pair_style lj/gromacs/coul/gromacs/omp command -============================================== +Accelerator Variants: *lj/gromacs/coul/gromacs/kk*, *lj/gromacs/coul/gromacs/omp* Syntax """""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index 544d13df9b34d1253f172e644bd2a3a33ad021b6..d0a7e69b009ab62f9c003b3dbdbaff4a5572f53f 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -1,4 +1,5 @@ .. index:: pair_style gw +.. index:: pair_style gw/zbl pair_style gw command ===================== diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 0d821fa946b753cca81707efe79cd029d53b7f0d..5e7183a3481a9985cf8a605f5c2f83b63411a063 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -1,16 +1,17 @@ .. index:: pair_style hbond/dreiding/lj +.. index:: pair_style hbond/dreiding/lj/omp +.. index:: pair_style hbond/dreiding/morse +.. index:: pair_style hbond/dreiding/morse/omp pair_style hbond/dreiding/lj command ==================================== -pair_style hbond/dreiding/lj/omp command -======================================== +Accelerator Variants: *hbond/dreiding/lj/omp* pair_style hbond/dreiding/morse command ======================================= -pair_style hbond/dreiding/morse/omp command -=========================================== +Accelerator Variants: *hbond/dreiding/morse/omp* Syntax """""" diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 924e19a8b3660f3fdd4bbb3965ffad8fb2eda48b..558c326175a5230b0b2c41fbb57c41b311c8a956 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -1,16 +1,17 @@ .. index:: pair_style hybrid +.. index:: pair_style hybrid/kk +.. index:: pair_style hybrid/overlay +.. index:: pair_style hybrid/overlay/kk pair_style hybrid command ========================= -pair_style hybrid/kk command -============================ +Accelerator Variants: *hybrid/kk* pair_style hybrid/overlay command ================================= -pair_style hybrid/overlay/kk command -==================================== +Accelerator Variants: *hybrid/overlay/kk* Syntax """""" diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index b8c5be3940f0593bea806e1f46b91e24aaffb882..22f0d0dd370efeefaa7b853ee8f8c39ad50abe75 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -5,7 +5,6 @@ .. index:: pair_style lj/cut/opt .. index:: pair_style lj/cut/omp - pair_style lj/cut command ========================= diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 7ea3c2c9c1a4144384516cd50f0963a8d7779ece..3f1172618b92ee7b89f48842c3242d498ee52644 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -1,13 +1,11 @@ .. index:: pair_style lj96/cut +.. index:: pair_style lj96/cut/gpu +.. index:: pair_style lj96/cut/omp pair_style lj96/cut command =========================== -pair_style lj96/cut/gpu command -=============================== - -pair_style lj96/cut/omp command -=============================== +Accelerator Variants: *lj96/cut/gpu*, *lj96/cut/omp* Syntax """""" diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index 800de20e6f1cd4a6780970ae03b338d66fd49fb6..e220e6e67c3a40f4071c70f4f286f587f58187a0 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -1,13 +1,11 @@ .. index:: pair_style lj/cubic +.. index:: pair_style lj/cubic/gpu +.. index:: pair_style lj/cubic/omp pair_style lj/cubic command =========================== -pair_style lj/cubic/gpu command -=============================== - -pair_style lj/cubic/omp command -=============================== +Accelerator Variants: *lj/cubic/gpu*, *lj/cubic/omp* Syntax """""" diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index ec34777d8dfddccfa8201f0cdbe64546f12e356b..f729c2016ea165c01d9eb1b7637f9d000adc2d38 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -30,7 +30,7 @@ Accelerator Variants: *lj/cut/coul/cut/gpu*, *lj/cut/coul/cut/kk*, *lj/cut/coul/ pair_style lj/cut/coul/debye command ==================================== -Accelerator Variants: *lj/cut/coul/debye/gpu*, lj/cut/coul/debye/kk, *lj/cut/coul/debye/omp* +Accelerator Variants: *lj/cut/coul/debye/gpu*, *lj/cut/coul/debye/kk*, *lj/cut/coul/debye/omp* pair_style lj/cut/coul/dsf command ================================== diff --git a/doc/src/pair_lj_cut_tip4p.rst b/doc/src/pair_lj_cut_tip4p.rst index 14e970a59eb291ac44f0ffbf4ed25fa5c419a26f..4f55f3b14e1e189472c9746560e1ff14e026ae10 100644 --- a/doc/src/pair_lj_cut_tip4p.rst +++ b/doc/src/pair_lj_cut_tip4p.rst @@ -5,7 +5,6 @@ .. index:: pair_style lj/cut/tip4p/long/omp .. index:: pair_style lj/cut/tip4p/long/opt - pair_style lj/cut/tip4p/cut command =================================== diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 8defbc36359ed8158626acc5ee16e28d1ffba90f..4d619a67e2f259417820b0794e1ad407c3659296 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -1,22 +1,19 @@ .. index:: pair_style lj/expand +.. index:: pair_style lj/expand/gpu +.. index:: pair_style lj/expand/kk +.. index:: pair_style lj/expand/omp +.. index:: pair_style lj/expand/coul/long +.. index:: pair_style lj/expand/coul/long/gpu pair_style lj/expand command ============================ -pair_style lj/expand/gpu command -================================ - -pair_style lj/expand/kk command -=============================== - -pair_style lj/expand/omp command -================================ +Accelerator Variants: *lj/expand/gpu*, *lj/expand/kk*, *lj/expand/omp* pair_style lj/expand/coul/long command ====================================== -pair_style lj/expand/coul/long/gpu command -========================================== +Accelerator Variants: *lj/expand/coul/long/gpu* Syntax """""" diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index ff6d834ad685edf9b9ae5cf475023b9e7bb72218..3609d093d99d7b7b1fa65c3fa5820e6e0c93a376 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -1,22 +1,19 @@ .. index:: pair_style lj/long/coul/long +.. index:: pair_style lj/long/coul/long/intel +.. index:: pair_style lj/long/coul/long/omp +.. index:: pair_style lj/long/coul/long/opt +.. index:: pair_style lj/long/tip4p/long +.. index:: pair_style lj/long/tip4p/long/omp pair_style lj/long/coul/long command ==================================== -pair_style lj/long/coul/long/intel command -========================================== - -pair_style lj/long/coul/long/omp command -======================================== - -pair_style lj/long/coul/long/opt command -======================================== +Accelerator Variants: *lj/long/coul/long/intel*, *lj/long/coul/long/omp*, *lj/long/coul/long/opt* pair_style lj/long/tip4p/long command ===================================== -pair_style lj/long/tip4p/long/omp command -========================================= +Accelerator Variants: *lj/long/tip4p/long/omp* Syntax """""" diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index 3137a17f730edef8945f2b062c61786f4e01315c..7ba12c89badc19bf2805a9bef9a4791669d486da 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -1,10 +1,10 @@ .. index:: pair_style lj/smooth +.. index:: pair_style lj/smooth/omp pair_style lj/smooth command ============================ -pair_style lj/smooth/omp command -================================ +Accelerator Variants: *lj/smooth/omp* Syntax """""" diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 833a4f035ddaee5e0123300c6fbe0da6de339777..b105fc49118fb5ae7664388ce9cca1b158c8e74e 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -1,10 +1,10 @@ .. index:: pair_style lj/smooth/linear +.. index:: pair_style lj/smooth/linear/omp pair_style lj/smooth/linear command =================================== -pair_style lj/smooth/linear/omp command -======================================= +Accelerator Variants: *lj/smooth/linear/omp* Syntax """""" diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 711f2576b3a6563fb49d7af4b61bc2f7475fadc7..e83a16c80b643f22ede75ef18782a765161075a5 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -1,16 +1,17 @@ .. index:: pair_style lubricate +.. index:: pair_style lubricate/omp +.. index:: pair_style lubricate/poly +.. index:: pair_style lubricate/poly/omp pair_style lubricate command ============================ -pair_style lubricate/omp command -================================ +Accelerator Variants: *lubricate/omp* pair_style lubricate/poly command ================================= -pair_style lubricate/poly/omp command -===================================== +Accelerator Variants: *lubricate/poly/omp* Syntax """""" diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index f4224ede47f0b0270400264f30443648bb2dc917..a9382556c52ed4eb7afd7e61b7d96daa886d5100 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -1,4 +1,5 @@ .. index:: pair_style lubricateU +.. index:: pair_style lubricateU/poly pair_style lubricateU command ============================= diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 1b46c51220aa26fe76ce137edabe1e9eb1322225..84d312e47c93de61d36511339bbe4346130babbc 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -1,4 +1,6 @@ .. index:: pair_style lj/mdf +.. index:: pair_style buck/mdf +.. index:: pair_style lennard/mdf pair_style lj/mdf command ========================= diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index bbba66c2b5031c4e77f5333feb18c50b9b9254c4..b5c94385fa4b3322a5783eb2ddb919d82576158f 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -1,10 +1,10 @@ .. index:: pair_style meam/spline +.. index:: pair_style meam/spline/omp pair_style meam/spline command ============================== -pair_style meam/spline/omp command -================================== +Accelerator Variants: *meam/spline/omp* Syntax """""" diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index 093eb707ad742d9f49ee972ff9f30306f46a72ec..1efdfa8b455b11f47a1ce896614a0e5671f7753e 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -1,4 +1,7 @@ .. index:: pair_style edpd +.. index:: pair_style mdpd +.. index:: pair_style mdpd/rhosum +.. index:: pair_style tdpd pair_style edpd command ======================= diff --git a/doc/src/pair_mesont_tpm.rst b/doc/src/pair_mesont_tpm.rst index f5b57893153f7f8fe1e27c92c5e98ab086f8c77c..e26f16fba34eb89840fde771fe475b9a1778dc55 100644 --- a/doc/src/pair_mesont_tpm.rst +++ b/doc/src/pair_mesont_tpm.rst @@ -1,7 +1,7 @@ .. index:: pair_style mesont/tpm pair_style mesont/tpm command -============================== +============================= Syntax """""" diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index 469817ee5e381474fece04be46d6a0566e537bbd..e1a34893c966e60772fcf34a098971bd2ebd891b 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -1,10 +1,10 @@ .. index:: pair_style mie/cut +.. index:: pair_style mie/cut/gpu pair_style mie/cut command ========================== -pair_style mie/cut/gpu command -============================== +Accelerator Variants: *mie/cut/gpu* Syntax """""" diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index 2b7e9cb90303c50d40733cf5eba66c1b0f015896..798df0bf7ad3773df74442e6b69fa72976fa7bb9 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -1,7 +1,7 @@ .. index:: pair_style mm3/switch3/coulgauss/long pair_style mm3/switch3/coulgauss/long command -============================================== +============================================= Syntax """""" diff --git a/doc/src/pair_morse.rst b/doc/src/pair_morse.rst index 1c8e731bc1f0bbb606fae9d1d9e54a8ea4ae5389..5ede37a916327842233fdebd649925b266c747ba 100644 --- a/doc/src/pair_morse.rst +++ b/doc/src/pair_morse.rst @@ -1,25 +1,20 @@ .. index:: pair_style morse +.. index:: pair_style morse/gpu +.. index:: pair_style morse/omp +.. index:: pair_style morse/opt +.. index:: pair_style morse/smooth/linear +.. index:: pair_style morse/smooth/linear/omp +.. index:: pair_style morse/kk pair_style morse command ======================== -pair_style morse/gpu command -============================ - -pair_style morse/omp command -============================ - -pair_style morse/opt command -============================ +Accelerator Variants: *morse/gpu*, *morse/omp*, *morse/opt*, *morse/kk* pair_style morse/smooth/linear command ====================================== -pair_style morse/smooth/linear/omp command -========================================== - -pair_style morse/kk command -=========================== +Accelerator Variants: *morse/smooth/linear/omp* Syntax """""" diff --git a/doc/src/pair_multi_lucy_rx.rst b/doc/src/pair_multi_lucy_rx.rst index 42a252519591e9966e7a70eec16127dfc6af8b4b..f6e6652271f2c0cded068c58f410d511fdd06721 100644 --- a/doc/src/pair_multi_lucy_rx.rst +++ b/doc/src/pair_multi_lucy_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style multi/lucy/rx +.. index:: pair_style multi/lucy/rx/kk pair_style multi/lucy/rx command ================================ -pair_style multi/lucy/rx/kk command -=================================== +Accelerator Variants: *multi/lucy/rx/kk* Syntax """""" diff --git a/doc/src/pair_nm.rst b/doc/src/pair_nm.rst index 7d7648cdc902a843889778b7b8783f04bf8d441e..d38e21fd1587c314cfeb0fd70c55ee9069128779 100644 --- a/doc/src/pair_nm.rst +++ b/doc/src/pair_nm.rst @@ -1,22 +1,24 @@ .. index:: pair_style nm/cut +.. index:: pair_style nm/cut/coul/cut +.. index:: pair_style nm/cut/coul/long +.. index:: pair_style nm/cut/omp +.. index:: pair_style nm/cut/coul/cut/omp +.. index:: pair_style nm/cut/coul/long/omp pair_style nm/cut command ========================= +Accelerator Variants: *nm/cut/omp* + pair_style nm/cut/coul/cut command ================================== +Accelerator Variants: *nm/cut/coul/cut/omp* + pair_style nm/cut/coul/long command =================================== -pair_style nm/cut/omp command -============================= - -pair_style nm/cut/coul/cut/omp command -====================================== - -pair_style nm/cut/coul/long/omp command -======================================= +Accelerator Variants: *nm/cut/coul/long/omp* Syntax """""" diff --git a/doc/src/pair_oxdna.rst b/doc/src/pair_oxdna.rst index c16e872ccfb2c04c457e98ceaa788448fb8a5aa2..4cc57868b4fe301d6559cf14dac41593d5ebba98 100644 --- a/doc/src/pair_oxdna.rst +++ b/doc/src/pair_oxdna.rst @@ -1,4 +1,8 @@ .. index:: pair_style oxdna/excv +.. index:: pair_style oxdna/stk +.. index:: pair_style oxdna/hbond +.. index:: pair_style oxdna/xstk +.. index:: pair_style oxdna/coaxstk pair_style oxdna/excv command ============================= diff --git a/doc/src/pair_oxdna2.rst b/doc/src/pair_oxdna2.rst index f63bec6a7f76017b0053f060c650198a59eaea14..ee01f2f488d5873dd8d79faada18eeb236b2ab4f 100644 --- a/doc/src/pair_oxdna2.rst +++ b/doc/src/pair_oxdna2.rst @@ -1,4 +1,9 @@ .. index:: pair_style oxdna2/excv +.. index:: pair_style oxdna2/stk +.. index:: pair_style oxdna2/hbond +.. index:: pair_style oxdna2/xstk +.. index:: pair_style oxdna2/coaxstk +.. index:: pair_style oxdna2/dh pair_style oxdna2/excv command ============================== diff --git a/doc/src/pair_oxrna2.rst b/doc/src/pair_oxrna2.rst index 05fd27b4a069f1913395dae6238db8e7fac71b56..831e4d9c4e1090a758c9f92aca692b76e7b7da10 100644 --- a/doc/src/pair_oxrna2.rst +++ b/doc/src/pair_oxrna2.rst @@ -1,4 +1,9 @@ .. index:: pair_style oxrna2/excv +.. index:: pair_style oxrna2/stk +.. index:: pair_style oxrna2/hbond +.. index:: pair_style oxrna2/xstk +.. index:: pair_style oxrna2/coaxstk +.. index:: pair_style oxrna2/dh pair_style oxrna2/excv command ============================== diff --git a/doc/src/pair_peri.rst b/doc/src/pair_peri.rst index de487df9a323bf81ba09a0d03e0cecfa54b66ff4..2a1c7f6aa5c24f6693e6b883549ce58c989bd31a 100644 --- a/doc/src/pair_peri.rst +++ b/doc/src/pair_peri.rst @@ -1,16 +1,19 @@ .. index:: pair_style peri/pmb +.. index:: pair_style peri/pmb/omp +.. index:: pair_style peri/lps +.. index:: pair_style peri/lps/omp +.. index:: pair_style peri/ves +.. index:: pair_style peri/eps pair_style peri/pmb command =========================== -pair_style peri/pmb/omp command -=============================== +Accelerator Variants: *peri/pmb/omp* pair_style peri/lps command =========================== -pair_style peri/lps/omp command -=============================== +Accelerator Variants: *peri/lps/omp* pair_style peri/ves command =========================== diff --git a/doc/src/pair_reaxc.rst b/doc/src/pair_reaxc.rst index 4d4368729ee2da2e6cf184098ce83ec217f37278..13ff16d4d3244f2dd90cff5f3d58b619aabeb13d 100644 --- a/doc/src/pair_reaxc.rst +++ b/doc/src/pair_reaxc.rst @@ -1,13 +1,11 @@ .. index:: pair_style reax/c +.. index:: pair_style reax/c/kk +.. index:: pair_style reax/c/omp pair_style reax/c command ========================= -pair_style reax/c/kk command -============================ - -pair_style reax/c/omp command -============================= +Accelerator Variants: *reax/c/kk*, *reax/c/omp* Syntax """""" diff --git a/doc/src/pair_resquared.rst b/doc/src/pair_resquared.rst index 33b40f6776168823178a244319d53fdc669fdbef..448af410db5adcf924523cac23f3251004468e33 100644 --- a/doc/src/pair_resquared.rst +++ b/doc/src/pair_resquared.rst @@ -1,13 +1,11 @@ .. index:: pair_style resquared +.. index:: pair_style resquared/gpu +.. index:: pair_style resquared/omp pair_style resquared command ============================ -pair_style resquared/gpu command -================================ - -pair_style resquared/omp command -================================ +Accelerator Variants: *resquared/gpu*, *resquared/omp* Syntax """""" diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_sdk.rst index 501ce6cd85e686b281febb216b0b6329e1f43855..541c53d37eca1c26f5d88a5a59a68faa229fdf24 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_sdk.rst @@ -1,31 +1,27 @@ .. index:: pair_style lj/sdk +.. index:: pair_style lj/sdk/gpu +.. index:: pair_style lj/sdk/kk +.. index:: pair_style lj/sdk/omp +.. index:: pair_style lj/sdk/coul/long +.. index:: pair_style lj/sdk/coul/long/gpu +.. index:: pair_style lj/sdk/coul/long/omp +.. index:: pair_style lj/sdk/coul/msm +.. index:: pair_style lj/sdk/coul/msm/omp pair_style lj/sdk command ========================= -pair_style lj/sdk/gpu command -============================= - -pair_style lj/sdk/kk command -============================ - -pair_style lj/sdk/omp command -============================= +Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* pair_style lj/sdk/coul/long command =================================== -pair_style lj/sdk/coul/long/gpu command -======================================= - -pair_style lj/sdk/coul/long/omp command -======================================= +Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* pair_style lj/sdk/coul/msm command ================================== -pair_style lj/sdk/coul/msm/omp command -====================================== +Accelerator Variants: *lj/sdk/coul/msm/omp* Syntax """""" diff --git a/doc/src/pair_smd_triangulated_surface.rst b/doc/src/pair_smd_triangulated_surface.rst index 9dbd66dcd87b6cb356ca58047280c074d7b586d8..1e3325486544084c9b1127165fa7c05fd09470d5 100644 --- a/doc/src/pair_smd_triangulated_surface.rst +++ b/doc/src/pair_smd_triangulated_surface.rst @@ -1,7 +1,7 @@ .. index:: pair_style smd/tri_surface pair_style smd/tri_surface command -=================================== +================================== Syntax """""" diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 6b3ee7f01971e90b50eece02fa60ef14694a805b..33946d464991830d8a9044a1f952ad936dcda3a9 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -1,7 +1,7 @@ .. index:: pair_style smd/ulsph pair_style smd/ulsph command -============================= +============================ Syntax """""" diff --git a/doc/src/pair_snap.rst b/doc/src/pair_snap.rst index 2ba2a9dd5819993ffb6b0f4d87f2eb30225c8ff4..8aa10f5986ad9c7503a08d4a249e67e81700fd6b 100644 --- a/doc/src/pair_snap.rst +++ b/doc/src/pair_snap.rst @@ -1,10 +1,10 @@ .. index:: pair_style snap +.. index:: pair_style snap/kk pair_style snap command ======================= -pair_style snap/kk command -========================== +Accelerator Variants: *snap/kk* Syntax """""" diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 294868f87235908d994db330ba737e01a18d87b2..cc024cb6ddcb895f5d332bc49468f3a23771bf11 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -1,13 +1,11 @@ .. index:: pair_style soft +.. index:: pair_style soft/gpu +.. index:: pair_style soft/omp pair_style soft command ======================= -pair_style soft/gpu command -=========================== - -pair_style soft/omp command -=========================== +Accelerator Variants: *soft/gpu*, *soft/omp* Syntax """""" diff --git a/doc/src/pair_spin_dipole.rst b/doc/src/pair_spin_dipole.rst index c86083f1e5605a5c2544ad54f752754a2c2a2f67..d1bbf3b699c33503ad9a246d9b6c2d4e6f37bfb2 100644 --- a/doc/src/pair_spin_dipole.rst +++ b/doc/src/pair_spin_dipole.rst @@ -1,4 +1,5 @@ .. index:: pair_style spin/dipole/cut +.. index:: pair_style spin/dipole/long pair_style spin/dipole/cut command ================================== diff --git a/doc/src/pair_spin_magelec.rst b/doc/src/pair_spin_magelec.rst index 5ef01ad10cda4e95648afb2e619f8b40646ae511..1860ed4677b3c30c49b3c6000299fdaef85b4926 100644 --- a/doc/src/pair_spin_magelec.rst +++ b/doc/src/pair_spin_magelec.rst @@ -1,7 +1,7 @@ .. index:: pair_style spin/magelec pair_style spin/magelec command -================================ +=============================== Syntax """""" diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index b673f652aaff5be18813c80bf96fa876fa796f37..bea417ed3d421133b4d7a82f434c38155342188a 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -1,19 +1,13 @@ .. index:: pair_style sw +.. index:: pair_style sw/gpu +.. index:: pair_style sw/intel +.. index:: pair_style sw/kk +.. index:: pair_style sw/omp pair_style sw command ===================== -pair_style sw/gpu command -========================= - -pair_style sw/intel command -=========================== - -pair_style sw/kk command -======================== - -pair_style sw/omp command -========================= +Accelerator Variants: *sw/gpu*, *sw/intel*, *sw/kk*, *sw/omp* Syntax """""" diff --git a/doc/src/pair_table.rst b/doc/src/pair_table.rst index 1a35cea7fdf11f4a6eb88ae75b0271f4d1be426a..39ed69055123617f715ec3fe217aaa5784e53dc3 100644 --- a/doc/src/pair_table.rst +++ b/doc/src/pair_table.rst @@ -1,16 +1,12 @@ .. index:: pair_style table +.. index:: pair_style table/gpu +.. index:: pair_style table/kk +.. index:: pair_style table/omp pair_style table command ======================== -pair_style table/gpu command -============================ - -pair_style table/kk command -=========================== - -pair_style table/omp command -============================ +Accelerator Variants: *table/gpu*, *table/kk*, *table/omp* Syntax """""" diff --git a/doc/src/pair_table_rx.rst b/doc/src/pair_table_rx.rst index 5545da22ef1abc27e947b43ddad4c4c984a8485e..9d23a479a3069ef5a74f76ef261d3b8766d820ca 100644 --- a/doc/src/pair_table_rx.rst +++ b/doc/src/pair_table_rx.rst @@ -1,10 +1,10 @@ .. index:: pair_style table/rx +.. index:: pair_style table/rx/kk pair_style table/rx command =========================== -pair_style table/rx/kk command -============================== +Accelerator Variants: *table/rx/kk* Syntax """""" diff --git a/doc/src/pair_tersoff.rst b/doc/src/pair_tersoff.rst index 251e12c87a1a5d5b26e882df4380cdd0dbd9180e..d9e5d60cd9fe4ff6488c85a34b525ba92bfc3083 100644 --- a/doc/src/pair_tersoff.rst +++ b/doc/src/pair_tersoff.rst @@ -1,25 +1,20 @@ .. index:: pair_style tersoff +.. index:: pair_style tersoff/table +.. index:: pair_style tersoff/gpu +.. index:: pair_style tersoff/intel +.. index:: pair_style tersoff/kk +.. index:: pair_style tersoff/omp +.. index:: pair_style tersoff/table/omp pair_style tersoff command ========================== -pair_style tersoff/table command -================================ - -pair_style tersoff/gpu command -============================== +Accelerator Variants: *tersoff/gpu*, *tersoff/intel*, *tersoff/kk*, *tersoff/omp* -pair_style tersoff/intel command +pair_style tersoff/table command ================================ -pair_style tersoff/kk command -============================= - -pair_style tersoff/omp command -============================== - -pair_style tersoff/table/omp command -==================================== +Accelerator Variants: *tersoff/table/omp* Syntax """""" diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 0426e65f14012b33d1f97a70aa374e4968f6e01e..7457541c183e175c5d14b8ea34d02839ea8861fc 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -1,22 +1,19 @@ .. index:: pair_style tersoff/mod +.. index:: pair_style tersoff/mod/c +.. index:: pair_style tersoff/mod/gpu +.. index:: pair_style tersoff/mod/kk +.. index:: pair_style tersoff/mod/omp +.. index:: pair_style tersoff/mod/c/omp pair_style tersoff/mod command ============================== +Accelerator Variants: *tersoff/mod/gpu*, *tersoff/mod/kk*, *tersoff/mod/omp* + pair_style tersoff/mod/c command ================================ -pair_style tersoff/mod/gpu command -================================== - -pair_style tersoff/mod/kk command -================================= - -pair_style tersoff/mod/omp command -================================== - -pair_style tersoff/mod/c/omp command -==================================== +Accelerator Variants: *tersoff/mod/c/omp* Syntax """""" diff --git a/doc/src/pair_tersoff_zbl.rst b/doc/src/pair_tersoff_zbl.rst index eff394d9a04eaf1f1947794166f8461cce0e5709..19e77ce8ebf6f2db8c3965582bdf3f7253cf9f3a 100644 --- a/doc/src/pair_tersoff_zbl.rst +++ b/doc/src/pair_tersoff_zbl.rst @@ -1,16 +1,12 @@ .. index:: pair_style tersoff/zbl +.. index:: pair_style tersoff/zbl/gpu +.. index:: pair_style tersoff/zbl/kk +.. index:: pair_style tersoff/zbl/omp pair_style tersoff/zbl command ============================== -pair_style tersoff/zbl/gpu command -================================== - -pair_style tersoff/zbl/kk command -================================= - -pair_style tersoff/zbl/omp command -================================== +Accelerator Variants: *tersoff/zbl/gpu*, *tersoff/zbl/kk*, *tersoff/zbl/omp* Syntax """""" diff --git a/doc/src/pair_thole.rst b/doc/src/pair_thole.rst index 9b05e06ceef98a8ebf4cb5169b49f7544b2bc867..a8cf8ee0449151c505365e8087dd40031fcfd7fa 100644 --- a/doc/src/pair_thole.rst +++ b/doc/src/pair_thole.rst @@ -1,4 +1,6 @@ .. index:: pair_style thole +.. index:: pair_style lj/cut/thole/long +.. index:: pair_style lj/cut/thole/long/omp pair_style thole command ======================== @@ -6,8 +8,7 @@ pair_style thole command pair_style lj/cut/thole/long command ==================================== -pair_style lj/cut/thole/long/omp command -======================================== +Accelerator Variants: *lj/cut/thole/long/omp* Syntax """""" diff --git a/doc/src/pair_ufm.rst b/doc/src/pair_ufm.rst index d9b08aaea22785baf138121a2c6e8c75084ebebc..140bb75ee7dd6ab7f41b500e4380b4e90bd50daf 100644 --- a/doc/src/pair_ufm.rst +++ b/doc/src/pair_ufm.rst @@ -1,16 +1,12 @@ .. index:: pair_style ufm +.. index:: pair_style ufm/gpu +.. index:: pair_style ufm/omp +.. index:: pair_style ufm/opt pair_style ufm command ====================== -pair_style ufm/gpu command -========================== - -pair_style ufm/omp command -========================== - -pair_style ufm/opt command -========================== +Accelerator Variants: *ufm/gpu*, *ufm/omp*, *ufm/opt* Syntax """""" diff --git a/doc/src/pair_vashishta.rst b/doc/src/pair_vashishta.rst index 0ad6cc35218aacb30a3dc1d0928faf9e9fcd3aea..aef401ec7cc7a60f0fb746a6ec49bfeb8966406e 100644 --- a/doc/src/pair_vashishta.rst +++ b/doc/src/pair_vashishta.rst @@ -1,22 +1,19 @@ .. index:: pair_style vashishta +.. index:: pair_style vashishta/gpu +.. index:: pair_style vashishta/omp +.. index:: pair_style vashishta/kk +.. index:: pair_style vashishta/table +.. index:: pair_style vashishta/table/omp pair_style vashishta command ============================ -pair_style vashishta/gpu command -================================ - -pair_style vashishta/omp command -================================ - -pair_style vashishta/kk command -=============================== +Accelerator Variants: *vashishta/gpu*, *vashishta/omp*, *vashishta/kk* pair_style vashishta/table command ================================== -pair_style vashishta/table/omp command -====================================== +Accelerator Variants: *vashishta/table/omp* Syntax """""" diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 079c19c3fd244a8465289009f7280143d6b4a6ce..057adbd60fe63ee57fa4a3282de0ac07718851e7 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -1,16 +1,12 @@ .. index:: pair_style yukawa +.. index:: pair_style yukawa/gpu +.. index:: pair_style yukawa/omp +.. index:: pair_style yukawa/kk pair_style yukawa command ========================= -pair_style yukawa/gpu command -============================= - -pair_style yukawa/omp command -============================= - -pair_style yukawa/kk command -============================ +Accelerator Variants: *yukawa/gpu*, *yukawa/omp*, *yukawa/kk* Syntax """""" diff --git a/doc/src/pair_yukawa_colloid.rst b/doc/src/pair_yukawa_colloid.rst index 78977118a1fc3331ebacc1f16aeb2293e8951e48..4d21d8e8c347e5ec9b2392959ee041b846ef989e 100644 --- a/doc/src/pair_yukawa_colloid.rst +++ b/doc/src/pair_yukawa_colloid.rst @@ -1,13 +1,11 @@ .. index:: pair_style yukawa/colloid +.. index:: pair_style yukawa/colloid/gpu +.. index:: pair_style yukawa/colloid/omp pair_style yukawa/colloid command ================================= -pair_style yukawa/colloid/gpu command -===================================== - -pair_style yukawa/colloid/omp command -===================================== +Accelerator Variants: *yukawa/colloid/gpu*, *yukawa/colloid/omp* Syntax """""" diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 5c256974840e5af591cf2abd7e261d5006ce7086..e01cbf45f21350e1c201f0b6f8ecfc67bf433483 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -1,16 +1,12 @@ .. index:: pair_style zbl +.. index:: pair_style zbl/gpu +.. index:: pair_style zbl/kk +.. index:: pair_style zbl/omp pair_style zbl command ====================== -pair_style zbl/gpu command -========================== - -pair_style zbl/kk command -========================= - -pair_style zbl/omp command -========================== +Accelerator Variants: *zbl/gpu*, *zbl/kk*, *zbl/omp* Syntax """""" diff --git a/doc/src/pg_developer.rst b/doc/src/pg_developer.rst index 95fc7ce51302435e3d514ba1bdf093231a487a87..5b929565d679534fb88525d5d252a62aaaca3d4a 100644 --- a/doc/src/pg_developer.rst +++ b/doc/src/pg_developer.rst @@ -10,11 +10,14 @@ of time and requests from the LAMMPS user community. LAMMPS source files =================== -The source files of the LAMMPS code are distributed across two -directories of the distribution. The core of the code is located in the -``src`` folder and its sub-directories. Almost all of those are C++ files -(implementation files have a ``.cpp`` extension and and headers a -``.h``). A sizable number of these files are in the ``src`` directory +The source files of the LAMMPS code are found in two +directories of the distribution: ``src`` and ``lib``. +Most of the code is C++ but there are small numbers of files +in several other languages. + +The core of the code is located in the +``src`` folder and its sub-directories. +A sizable number of these files are in the ``src`` directory itself, but there are plenty of :doc:`packages `, which can be included or excluded when LAMMPS is built. See the :doc:`Include packages in build ` section of the manual for more @@ -25,7 +28,7 @@ enabled or disabled for a LAMMPS binary. The source files for each package are in all-uppercase sub-directories of the ``src`` folder, for example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS`` sub-directory is not a package but contains a dummy MPI library, that is -used when building a serial version of the code. the ``src/MAKE`` +used when building a serial version of the code. The ``src/MAKE`` directory contains makefiles with settings and flags for a variety of configuration and machines for the build process with traditional makefiles. @@ -39,7 +42,8 @@ or CUDA. These libraries are linked to during a LAMMPS build, if the corresponding package is installed. LAMMPS C++ source files almost always come in pairs, such as -``src/run.cpp`` and ``src/run.h``. The pair of files defines a C++ +``src/run.cpp`` (implementation file) and ``src/run.h`` (header file). +Each pair of files defines a C++ class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the :doc:`run ` command in a LAMMPS input script. As this example illustrates, source file and class names often have a @@ -48,6 +52,9 @@ Some source files and classes do not have a corresponding input script command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force` class. They are discussed in the next section. +A small number of C++ classes and utility functions are implemented with +only a ``.h`` file. Examples are the Pointer class and the mergesort function. + LAMMPS class topology ===================== diff --git a/doc/src/pg_lib_add.rst b/doc/src/pg_lib_add.rst index 139476c68334b0f798d6e8746a5eac951ff90106..e58b6c2b7352a3e4ef02cb1dca61e50be5b140b0 100644 --- a/doc/src/pg_lib_add.rst +++ b/doc/src/pg_lib_add.rst @@ -12,7 +12,7 @@ there are now a few requirements for inclusion of changes. implement functionality that can already be achieved with the existing APIs. - All changes and additions should be documented with - `Doxygen `_ style comments and references + `Doxygen `_ style comments and references to those functions added to the corresponding files in the ``doc/src`` folder. - If possible, new unit tests to test those new features should diff --git a/doc/src/pg_python.rst b/doc/src/pg_python.rst index 72d07c598311390f3501bea14534b7c1f586023f..80e83d4638de270fc3f39eab419fb41bdf19283d 100644 --- a/doc/src/pg_python.rst +++ b/doc/src/pg_python.rst @@ -14,7 +14,7 @@ There are multiple Python interface classes in the :py:mod:`lammps` module: - the :py:class:`lammps ` class. This is a wrapper around the C-library interface and its member functions try to replicate the - :doc:`C-library API ` closely. This is the most + :ref:`C-library API ` closely. This is the most feature-complete Python API. - the :py:class:`PyLammps ` class. This is a more high-level and more Python style class implemented on top of the @@ -63,7 +63,7 @@ MPI ranks after splitting the communicator. Here is a simple example: # explicitly close and delete LAMMPS instance (optional) lmp.close() -Same as with the :doc:`C library API ` this will use the +Same as with the :ref:`C library API ` this will use the ``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was compiled with. The :py:func:`lmp.close() ` call is optional since the LAMMPS class instance will also be deleted @@ -113,8 +113,8 @@ The ``lammps`` class API ************************ The :py:class:`lammps ` class is the core of the LAMMPS -Python interfaces. It is a wrapper around the :doc:`LAMMPS C library -API ` using the `Python ctypes module +Python interfaces. It is a wrapper around the :ref:`LAMMPS C library +API ` using the `Python ctypes module `_ and a shared library compiled from the LAMMPS sources code. The individual methods in this class try to closely follow the corresponding C functions. The handle diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 603f312e9d3f10209ae39747c36733900b8da8d7..f9a7d3e39a2f75e09e70054975e3039057f86e23 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -60,6 +60,7 @@ reader = {} region = {} total = 0 +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$") style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)") upper = re.compile("[A-Z]+") gpu = re.compile("(.+)/gpu$") @@ -70,6 +71,26 @@ omp = re.compile("(.+)/omp$") opt = re.compile("(.+)/opt$") removed = re.compile("(.*)Deprecated$") +def load_index_entries_in_file(path): + entries = [] + with open(path, 'r') as reader: + for line in reader: + m = index_pattern.match(line) + if m: + command_type = m.group(1) + style = m.group(2) + entries.append((command_type, style)) + return entries + +def load_index_entries(): + index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(), + 'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()} + rst_files = glob(os.path.join(doc_dir, '*.rst')) + for f in rst_files: + for command_type, style in load_index_entries_in_file(f): + index[command_type].add(style) + return index + def register_style(styles, name, info): if name in styles: for key, value in info.items(): @@ -112,6 +133,24 @@ def check_style(filename, dirname, pattern, styles, name, suffix=False, skip=set counter += 1 return counter +def check_style_index(name, styles, index, skip=[]): + counter = 0 + for style in styles: + if style not in index and not styles[style]['removed'] and style not in skip: + print(f"{name} index entry {style} is missing") + counter += 1 + + for suffix in styles[style]: + if suffix == 'removed': continue + if suffix == 'kokkos': + suffix_style = f"{style}/kk" + else: + suffix_style = f"{style}/{suffix}" + if styles[style][suffix] and suffix_style not in index and style not in skip: + print(f"{name} index entry {suffix_style} is missing") + counter += 1 + return counter + for header in headers: if verbose: print("Checking ", header) with open(header) as f: @@ -207,6 +246,13 @@ Total number of styles (including suffixes): %d""" \ len(fix), len(improper), len(integrate), len(kspace), \ len(minimize), len(pair), len(reader), len(region), total)) +index = load_index_entries() + +total_index = 0 +for command_type, entries in index.items(): + total_index += len(entries) + +print("Total number of style index entries:", total_index) counter = 0 @@ -244,5 +290,18 @@ counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) 0: + # override original file + shutil.move(new_file, orig_file) + else: + os.remove(new_file) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index a9f976c3fd56f0b9feb22bf394f1f327dd263177..586e14da880457d64ee09cdc7ac08a1ca538ceab 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1355,6 +1355,7 @@ iva Ivanov Ivector Iw +iwyu ixcm ixx Ixx diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h index 80942f60bfa6a300b50f48cc7f1e1c50edb5521a..7bf6125bc6f5fab4e488748510cb9b440de144a0 100644 --- a/lib/awpmd/ivutils/include/logexc.h +++ b/lib/awpmd/ivutils/include/logexc.h @@ -273,7 +273,7 @@ public: }; /// format a string -const char *fmt(const char *format,...); +const char *logfmt(const char *format,...); /// macros with common usage #define LOGFATAL(code,text,lineinfo) ((lineinfo) ? ::message(vblFATAL,(code)," %s at %s:%d",(text),__FILE__,__LINE__) : \ diff --git a/lib/awpmd/ivutils/src/logexc.cpp b/lib/awpmd/ivutils/src/logexc.cpp index d29745fda13efb7a9a632d2712310c951df9031f..7e82af0f659aec5be08f1f68ec61f402796899d6 100644 --- a/lib/awpmd/ivutils/src/logexc.cpp +++ b/lib/awpmd/ivutils/src/logexc.cpp @@ -16,7 +16,7 @@ message_logger &message_logger::global(){ message_logger *message_logger::glogp=NULL; stdfile_logger default_log("",0,stdout,stderr,vblALLBAD|vblMESS1,vblFATAL,1); -const char *fmt(const char *format,...){ +const char *logfmt(const char *format,...){ va_list args; va_start(args,format); static char buff[1024]; diff --git a/lib/awpmd/systems/interact/TCP/wpmd.cpp b/lib/awpmd/systems/interact/TCP/wpmd.cpp index 1e53f3141c747d7a64ad7a9f88784b68b278747c..660d7c21d72ad405eb69dfc8dae81eeb6c16e42a 100644 --- a/lib/awpmd/systems/interact/TCP/wpmd.cpp +++ b/lib/awpmd/systems/interact/TCP/wpmd.cpp @@ -170,7 +170,7 @@ int AWPMD::set_pbc(const Vector_3P pcell, int pbc_){ int AWPMD::set_electrons(int s, int n, Vector_3P x, Vector_3P v, double* w, double* pw, double mass, double *q) { if(s < 0 || s > 1) - return LOGERR(-1,fmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD.set_electrons: invaid s setting (%d)!",s),LINFO); norm_matrix_state[s] = NORM_UNDEFINED; nwp[s]=ne[s]=n; @@ -363,20 +363,20 @@ int AWPMD::interaction(int flag, Vector_3P fi, Vector_3P fe_x, //3. inverting the overlap matrix int info=0; if(nes){ - /*FILE *f1=fopen(fmt("matrO_%d.d",s),"wt"); + /*FILE *f1=fopen(logfmt("matrO_%d.d",s),"wt"); fileout(f1,Y[s],"%15g"); fclose(f1);8*/ - + ZPPTRF("L",&nes,Y[s].arr,&info); // analyze return code here if(info<0) - return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); + return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRF failed (exitcode %d)!",info),LINFO); ZPPTRI("L",&nes,Y[s].arr,&info); if(info<0) - return LOGERR(info,fmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); + return LOGERR(info,logfmt("AWPMD.interacton: call to ZPTRI failed (exitcode %d)!",info),LINFO); - - /*f1=fopen(fmt("matrY_%d.d",s),"wt"); + + /*f1=fopen(logfmt("matrY_%d.d",s),"wt"); fileout(f1,Y[s],"%15g"); fclose(f1);*/ } @@ -758,7 +758,7 @@ void AWPMD::norm_factorize(int s) { int nes8 = ne[s]*8, info; DGETRF(&nes8, &nes8, Norm[s].arr, &nes8, &ipiv[0], &info); if(info < 0) - LOGERR(info,fmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); + LOGERR(info,logfmt("AWPMD.norm_factorize: call to DGETRF failed (exitcode %d)!",info),LINFO); norm_matrix_state[s] = NORM_FACTORIZED; } @@ -773,7 +773,7 @@ void AWPMD::norm_invert(int s) { DGETRI(&nes8, Norm[s].arr, &nes8, &ipiv[0], (double*)IDD.arr, &IDD_size, &info); // use IDD for work storage if(info < 0) - LOGERR(info,fmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); + LOGERR(info,logfmt("AWPMD.norm_invert: call to DGETRI failed (exitcode %d)!",info),LINFO); norm_matrix_state[s] = NORM_INVERTED; } @@ -829,7 +829,7 @@ int AWPMD::step(double dt){ //e gets current electronic coordinates int AWPMD::get_electrons(int spin, Vector_3P x, Vector_3P v, double* w, double* pw, double mass){ if(spin<0 || spin >1) - return -1; // invalid spin: return LOGERR(-1,fmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO); + return -1; // invalid spin: return LOGERR(-1,logfmt("AWPMD.get_electrons: invaid spin setting (%d)!",spin),LINFO); if(mass<0) mass=me; for(int i=0;i 1) - return LOGERR(-1,fmt("AWPMD_split.set_electrons: invaid spin setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD_split.set_electrons: invaid spin setting (%d)!",s),LINFO); // calculating the total n nvar[s]=0; @@ -68,22 +68,22 @@ int AWPMD_split::set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* norm_matrix_state[s] = NORM_UNDEFINED; ne[s]=nel; wp[s].resize(n); - + split_c[s].resize(n); split_c[s].assign(c,c+n); - - + + nspl[s].resize(nel); nspl[s].assign(splits,splits+nel); partition1[s].clear(); for(int i=0;i0){ // width PBC, keeping the width are within [0,Lextra] w[i]=fmod(w[i],Lextra); @@ -107,7 +107,7 @@ int AWPMD_split::set_electrons(int s, int nel, Vector_3P x, Vector_3P v, double* else qe[s].assign(nwp[s],-1); - + return 1; } @@ -121,40 +121,40 @@ void AWPMD_split::eterm_deriv(int ic1,int s1,int c1, int j1,int ic2,int s2, int cdouble ck(split_c[s2][ic2+k2][0],split_c[s2][ic2+k2][1]); int indw1=8*ic1, indw2=8*ic2; int indn1=(nvar[s1]/10)*8+2*ic1, indn2=(nvar[s2]/10)*8+2*ic2; - cdouble part_jk=conj(cj)*ck; + cdouble part_jk=conj(cj)*ck; int M= 1; //(j1==k2 ? 1 : 2); // over a_k_re - E_der[s2][indw2+8*k2]+= M*real(pref*part_jk*(o.da2_re()*v+o.I0*dv_ak)); + E_der[s2][indw2+8*k2]+= M*real(pref*part_jk*(o.da2_re()*v+o.I0*dv_ak)); // over a_k_im - E_der[s2][indw2+8*k2+1]+= M*real(pref*part_jk*(o.da2_im()*v+i_unit*o.I0*dv_ak)); + E_der[s2][indw2+8*k2+1]+= M*real(pref*part_jk*(o.da2_im()*v+i_unit*o.I0*dv_ak)); // over a_j_re - E_der[s1][indw1+8*j1]+= M*real(pref*part_jk*(o.da1_re()*v+o.I0*dv_aj_conj)); + E_der[s1][indw1+8*j1]+= M*real(pref*part_jk*(o.da1_re()*v+o.I0*dv_aj_conj)); // over a_j_im - E_der[s1][indw1+8*j1+1]+= M*real(pref*part_jk*(o.da1_im()*v-i_unit*o.I0*dv_aj_conj)); + E_der[s1][indw1+8*j1+1]+= M*real(pref*part_jk*(o.da1_im()*v-i_unit*o.I0*dv_aj_conj)); for(int i=0;i<3;i++){ // over b_k_re - E_der[s2][indw2+8*k2+2+2*i]+= M*real(pref*part_jk*(o.db2_re(i)*v+o.I0*dv_bk[i])); + E_der[s2][indw2+8*k2+2+2*i]+= M*real(pref*part_jk*(o.db2_re(i)*v+o.I0*dv_bk[i])); // over b_k_im - E_der[s2][indw2+8*k2+2+2*i+1]+= M*real(pref*part_jk*(o.db2_im(i)*v+i_unit*o.I0*dv_bk[i])); + E_der[s2][indw2+8*k2+2+2*i+1]+= M*real(pref*part_jk*(o.db2_im(i)*v+i_unit*o.I0*dv_bk[i])); // over b_j_re - E_der[s1][indw1+8*j1+2+2*i]+= M*real(pref*part_jk*(o.db1_re(i)*v+o.I0*dv_bj_conj[i])); + E_der[s1][indw1+8*j1+2+2*i]+= M*real(pref*part_jk*(o.db1_re(i)*v+o.I0*dv_bj_conj[i])); // over b_j_im - E_der[s1][indw1+8*j1+2+2*i+1]+= M*real(pref*part_jk*(o.db1_im(i)*v-i_unit*o.I0*dv_bj_conj[i])); + E_der[s1][indw1+8*j1+2+2*i+1]+= M*real(pref*part_jk*(o.db1_im(i)*v-i_unit*o.I0*dv_bj_conj[i])); } // over ck_re - E_der[s2][indn2+2*k2]+=M*real(pref*conj(cj)*o.I0*v); + E_der[s2][indn2+2*k2]+=M*real(pref*conj(cj)*o.I0*v); // over ck_im E_der[s2][indn2+2*k2+1]+=M*real(pref*i_unit*conj(cj)*o.I0*v); // over cj_re - E_der[s1][indn1+2*j1]+=M*real(pref*ck*o.I0*v); + E_der[s1][indn1+2*j1]+=M*real(pref*ck*o.I0*v); // over cj_im - E_der[s1][indn1+2*j1+1]+=M*real(-pref*i_unit*ck*o.I0*v); - + E_der[s1][indn1+2*j1+1]+=M*real(-pref*i_unit*ck*o.I0*v); + double t= -M*real(pref*part_jk*o.I0*v); // nonlocal terms: TODO: make a separate global loop for summation of nonlocal terms for(int j=0;j -mu, v -> -v !!! } - - + + for(int k1=j1+1;k1(E_der[s1].begin()+indw1,(double *)&fe_x[iv1+k1],(double *)&fe_p[iv1+k1],&fe_w[iv1+k1],&fe_pw[iv1+k1], 1./one_h); @@ -341,14 +341,14 @@ void AWPMD_split::get_el_forces(int flag, Vector_3P fe_x, ic1+=nspl[s1][c1]; // incrementing block1 wp address iv1+=nspl[s1][c1]; // incrementing global variable address } - } + } } } //e same as interaction, but using Hartee factorization (no antisymmetrization) -int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, +int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, Vector_3P fe_p, double *fe_w, double *fe_pw, Vector_2P fe_c){ - + // resize arrays if needed enum APPROX tmp=HARTREE; swap(tmp,approx); // do not need large matrices @@ -358,39 +358,39 @@ int AWPMD_split::interaction_hartree(int flag, Vector_3P fi, Vector_3P fe_x, // clearing forces clear_forces(flag,fi,fe_x,fe_p,fe_w,fe_pw,fe_c); // calculate block norms and (optionally) derivatives - calc_norms(flag); + calc_norms(flag); Eee = Ew = 0.; for(int s1=0;s1<2;s1++){ Ee[s1]=0.; Eei[s1]=0.; int ic1=0; // starting index of the wp for current electron - + for(int c1=0;c1 1) - return LOGERR(-1,fmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO); + return LOGERR(-1,logfmt("AWPMD_split.add_electron: invaid spin setting (%d)!",s),LINFO); s_add=s; spl_add=0; return ne[s_add]; diff --git a/src/ASPHERE/compute_erotate_asphere.cpp b/src/ASPHERE/compute_erotate_asphere.cpp index 3cf23b87eb70dcaf2c1678af126c5548452d87bb..945b91fbbd8fcf5b4641977177d35cb293c3d0f8 100644 --- a/src/ASPHERE/compute_erotate_asphere.cpp +++ b/src/ASPHERE/compute_erotate_asphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_asphere.h" -#include + #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 4350678bbda235c4546254c5603e5b09a005c736..889563f617205bd5f80f916c947486f2c4a85430 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_asphere.h" -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp index 0501ea1e8ad4e5c5ad173f31798cfa74453438b4..6d1727ce45947fa517cb22eb741b4b84be910f29 100644 --- a/src/ASPHERE/fix_nph_asphere.cpp +++ b/src/ASPHERE/fix_nph_asphere.cpp @@ -13,7 +13,7 @@ #include "fix_nph_asphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp index f7f253f40b65591c9dca867dfc8a70d1b74912eb..064a20d55b2e82e87e692644bbb8c7890d90155a 100644 --- a/src/ASPHERE/fix_npt_asphere.cpp +++ b/src/ASPHERE/fix_npt_asphere.cpp @@ -13,7 +13,7 @@ #include "fix_npt_asphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp index e0275d4acf9a0c900e4c69c76823b2c0b1205372..d439d947bff1cba20f3f776ae5eaffd27211b52d 100644 --- a/src/ASPHERE/fix_nvt_asphere.cpp +++ b/src/ASPHERE/fix_nvt_asphere.cpp @@ -13,11 +13,11 @@ #include "fix_nvt_asphere.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 064e365dc163824f188d9913302857cd06debf02..89350dd00f3858df6ff4fb28cefc8a614bd15829 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gayberne.h" -#include + #include #include "math_extra.h" #include "atom.h" @@ -28,7 +28,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index a1c64775428600a999d233813a03d450d754d617..6397e77f5bf4c564015baedb2e424e0e0cd22782 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -20,7 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index a25addaba4297b15b2ee17adf85179a04a152ca0..81fb4d4b6ca1324556f89bcf767ff6c0b8910844 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_resquared.h" -#include + #include #include "math_extra.h" #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 0f840dadf36a550f52babfbe0b2bb2fd916bd3c0..cf89cf9d33ed57a0648e00c490fbe7e961792fd0 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp index a99c025e1f370168b597868dbed22cc5982f2b91..e63d50f81473339aa6728c46fae0677693d24184 100644 --- a/src/BODY/body_nparticle.cpp +++ b/src/BODY/body_nparticle.cpp @@ -12,16 +12,15 @@ ------------------------------------------------------------------------- */ #include "body_nparticle.h" -#include -#include -#include "my_pool_chunk.h" -#include "math_extra.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" -#include "memory.h" +#include "atom_vec_body.h" #include "error.h" -#include "fmt/format.h" +#include "math_extra.h" +#include "memory.h" +#include "my_pool_chunk.h" + +#include using namespace LAMMPS_NS; diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 349ad957c2eb76ffab55b5f4bbb40e407edc0459..c43484dca227d84904426c994ba855943938d94e 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polygon.h" -#include -#include -#include "my_pool_chunk.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" +#include "atom_vec_body.h" #include "domain.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "my_pool_chunk.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index cb84517b6f6c473fe3b23cf1d53d78eb77d66cff..18fd65c1dd281f9fb32ae495d3a59560069f0712 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "body_rounded_polyhedron.h" -#include -#include -#include -#include "my_pool_chunk.h" -#include "atom_vec_body.h" + #include "atom.h" -#include "force.h" +#include "atom_vec_body.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "my_pool_chunk.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp index 915407db9249e9863999f56c2e5f26c5d1a24b43..cf570d71a3d686ada151eef32f69a17c6d9b03e8 100644 --- a/src/BODY/compute_body_local.cpp +++ b/src/BODY/compute_body_local.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "compute_body_local.h" -#include -#include + #include "atom.h" #include "atom_vec_body.h" #include "body.h" -#include "update.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp index 4cf9ac5009a766ece966207a9e3701b3b4130b4c..18c301678a606e0f895672906fa4aea415e3141f 100644 --- a/src/BODY/compute_temp_body.cpp +++ b/src/BODY/compute_temp_body.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_body.h" -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp index 1e8cc88e7c0bd62b710d39afa1c3f0e036693b86..f198919ad8455762d5423e4428acdbaf1e6cf6c4 100644 --- a/src/BODY/fix_nph_body.cpp +++ b/src/BODY/fix_nph_body.cpp @@ -17,11 +17,11 @@ #include "fix_nph_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp index 295777753f14a869dc3cba6139399b7354964d82..23194bc8caddf8d218c55ece70916ffe55ced0c0 100644 --- a/src/BODY/fix_npt_body.cpp +++ b/src/BODY/fix_npt_body.cpp @@ -17,11 +17,11 @@ #include "fix_npt_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp index 458ff1ab14c050c634ffd60881509bde57208a82..3cab4416b0440f0281ce209c115cee97657abf1b 100644 --- a/src/BODY/fix_nvt_body.cpp +++ b/src/BODY/fix_nvt_body.cpp @@ -17,11 +17,11 @@ #include "fix_nvt_body.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index b3333d4715043f2242b28743925a3e034a0083be..ece23d9522b17bf4b12dbdcb9123198359525506 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -23,7 +23,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 9687c28613e8ccce0120710ba4ed4bfcde1bb7f0..fa5a8e57dab4556c91b0fda6f5540a5441a3f518 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polygon.h" -#include + #include #include #include "math_extra.h" @@ -34,7 +34,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index dfefc318afe948ccc17bb9f0f6337ef39acd2569..d376ac759eba9a1c3b680d7e4f40e5266a799247 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -21,7 +21,7 @@ ------------------------------------------------------------------------- */ #include "pair_body_rounded_polyhedron.h" -#include + #include #include #include "atom.h" @@ -37,7 +37,7 @@ #include "error.h" #include "math_extra.h" #include "math_const.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 431479b489fc0ea1481dd0591fbbaff005efde76..eea43480e194779d08573bc99ae68874a7387601 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_class2.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index 2cd63eafcb8a3b119ba03c75736eb8a603fa82b9..a97b06a3c770ff71f3e242c3e9e45aff9cc8e4bc 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -17,7 +17,7 @@ #include #include "bond_class2.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index 44d4902e4a2584cd4495a4306ee32b8c984831af..5be522f2c9936eccfc248000044c546240dde379 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 662459abb7a57662a343ee8ac8d3cac8a01562d7..0b07a7d60c4ebaec10101f425e0bdc8bdf8bc2b9 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_class2.h" -#include + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 96b035f83b1f583a9b276c2632ce22559eead7aa..bb1dfe0ab30c79ecdb5f0b2f0fe956a056f46ea3 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -10,7 +10,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 9aca9f048a57c0b7611156f7f5c78b72d3957056..8375043ed8e9dbaa01273b4d1d55d0048d0b7518 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index 5c7c107d023ff207271438824f487d3ee140bc07..3b9ef8deaf092a411e5316984a06e106f35004bc 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp index 58593a99b18baef1c414ce3d8822d3c2409df629..ef5bfb72e16f9a23d260628f443b570182620bf3 100644 --- a/src/COLLOID/fix_wall_colloid.cpp +++ b/src/COLLOID/fix_wall_colloid.cpp @@ -16,10 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_wall_colloid.h" -#include + #include #include "atom.h" -#include "atom_vec.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index d7b2dba14a0db0ae79a2c0aaa349e0eb73982c67..786be66c70569ce7d7118e16f21a3feaff540fcf 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_brownian.h" -#include + #include #include #include "atom.h" @@ -36,7 +36,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index c3eb4f28a5afb21543005085f6e256580e5cecff..9c2593ffb1af8a6020805cb6ceb687fcdb602067 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_brownian_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index 7552d123c33b19a5d8f8c56dbf17c3b98e590624..f95645c6131d46076436f141993c035145298916 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_colloid.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index 4f2a4455a3c7a6bbefee3c263ab71eaeed395950..867bb9197979b60557c7a83adc2ba7f23873e1f0 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate.h" -#include + #include #include #include "atom.h" @@ -35,7 +35,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 4fb16116609b32dcd691d0f54d4b72cbc9782a0b..2df1ecaaa62c7f6c3c818712c7b2f3002c1694ae 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricateU.h" -#include + #include #include #include "atom.h" @@ -34,7 +34,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 7fd847671ea067331c20f07643df06f51b8e51b4..8483bb0f51161c047dd95c75dc5486f6df83a5d1 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricateU_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index e347441cf4a8a226c46f7b44342ac3e6e7e15db6..351757e09b82e9f21ecb823c1a54acff12939fbb 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lubricate_poly.h" -#include + #include #include #include "atom.h" diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 6c78ba7910bdcdd77aa3c8d67c28fdc4e29abaad..484175762e7d9c0888103a53e797814b0513c314 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index a8da9a1a2c7d52ca874f141a78434260e0c55dfc..8fb08db3c8508ddc4eed35a5b4d09cfb38afd55d 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -17,14 +17,14 @@ #ifdef LAMMPS_ZSTD -#include "dump_atom_zstd.h" #include "domain.h" +#include "dump_atom_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" -#include "utils.h" #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 2d48e02f3cd02c600a73a9a9de9cbfeec05c708a..18f0fa56d7315452bf37ee7c40ed07b72fb0f713 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -16,10 +16,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 0f74e2550b77f845b7bf9933762344a3fc442fff..5948a3f83e4f7143d4bb26b94953c6e0e085e580 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -16,15 +16,15 @@ ------------------------------------------------------------------------- */ #ifdef LAMMPS_ZSTD -#include "dump_cfg_zstd.h" + #include "atom.h" #include "domain.h" +#include "dump_cfg_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" -#include "utils.h" #include -#include "fmt/format.h" using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 35a2d25a2a5d09190e7a88731e1952259e38ad19..fb2b121f7f873c6b878f5762f4566ef9993d2653 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index 395ba51fdcde3ab6465d932e3d10c8dabff8f0b8..c7ede3b38ceadd5602691f07ef2ec7d7d476dc48 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -17,14 +17,14 @@ #ifdef LAMMPS_ZSTD -#include "dump_custom_zstd.h" #include "domain.h" +#include "dump_custom_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" -#include "utils.h" #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index a346de31277ba47ca22e1538551b6feaccefcabb..49a3c3bef2d727732be5230b9c746854f006bbe0 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -15,10 +15,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 3e658fd0702135ceb9982acbf7434e31f9eae4ba..9393654dd63857c5387e0bcf6d2f266edbadb075 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -21,10 +21,10 @@ #include "domain.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 79d2d209972223e3c6d669245005e45a0b6b3500..cc07b1ce61808f1643fd6165eeb60fe648f20402 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -14,10 +14,10 @@ #include "dump_xyz_gz.h" #include "error.h" #include "update.h" -#include "utils.h" + #include -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 066609eebbafc32ca561b85fad04ffb2f4558166..eb0600f34b3db62824c2301da696bea0939cdfc5 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -19,11 +19,10 @@ #include "dump_xyz_zstd.h" #include "error.h" +#include "file_writer.h" #include "update.h" -#include "utils.h" #include -#include "fmt/format.h" using namespace LAMMPS_NS; diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp index d8f952551d83016438af63c4c9107e6c144695e7..1b7eb1e43f5fce64afbc942f77490d55540da41f 100644 --- a/src/CORESHELL/compute_temp_cs.cpp +++ b/src/CORESHELL/compute_temp_cs.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "compute_temp_cs.h" -#include + #include -#include + #include "atom.h" #include "atom_vec.h" #include "domain.h" @@ -31,7 +31,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp index b6895be3012fdfa58edc937fef4840d2fb695f9e..4193b5c6a864265640938c7fa1b8a08ebc19e1bd 100644 --- a/src/DIPOLE/atom_vec_dipole.cpp +++ b/src/DIPOLE/atom_vec_dipole.cpp @@ -12,15 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_dipole.h" -#include + #include "atom.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "memory.h" -#include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 8f91420043ff892a7bd80d17a1f33094727ac40b..25fed599db048a62bae66ccf117addde3b7b1fcb 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 73aa628296e45acdf44e89ab409490dbae80138b..67d2e0aa3ceca1802661904a2f1d692dd487c987 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_dipole_long.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index f7c8251e79e570796117fcb40ba56988f1223919..86e143626df0db59c62ec708c88716f33af55218 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_dipole_long.h" -#include + #include #include #include "math_const.h" @@ -30,7 +30,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 0552d23cdbe6492a91f41d13a3b01955508314de..15bc42c37ec46c6f5d3169848e8cff86318655ed 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -13,7 +13,7 @@ #include "fix_gpu.h" #include -#include + #include "atom.h" #include "force.h" #include "pair.h" @@ -30,7 +30,7 @@ #include "neighbor.h" #include "citeme.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index 28386f5fd5469d7ddccd5a5317e0d46c5a3d9cb6..86467f49c0ac6efc6e8a03aca1174fab54ffa227 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_beck_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 8bc99a3d4902e2f2e862cf89b0ff766e9e1ce2fa..c27c670f2ac276dd6b4e868d12d2ebc7dec71825 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_long_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index 5dd4c3421f8b8b5ee3b54ea80ea3f58741250d9d..a2524909e5dc6350ee188c48fd95625b3d331ede 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 4ba28c25aa02dd793080af7e33bbb7510293c8f3..cf54b72cf584e17e5810cbc5d22f78dd676539d8 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_wolf_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index b5e0edea6d29ad2ad6400b5d420ba5facb20310e..e9aa951236d41be5fcec8bcd8a4b70037ee7cb1b 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_coul_wolf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index a5e94389b6a1b9d740162a44bc57f46c6b92b2e5..5a5a6d2a363b91838d98031730bcd24a5ec61b95 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_born_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index 1a5479ea1d6ae2d0abecdc3abf0ad4085e0498eb..de9f0d1ebad6de471f68b3af366510bff2957abc 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index 221e178b57b6038b6857d5a52f201a3b3e11664c..41823fc27eda3dd7df7118b433f0790e28307080 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 07107750e63c3c1d5d0ab7600ff3cc8e97e598c3..1f7abc06bc4998b02559ab589ca5292a1156e4d4 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_buck_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index a7cafbe75a05d51b09e2e950ed536fc9dfbf3d80..39737ab18311679518db77ed954d38f891f5f2ee 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_colloid_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index bacbdbb1a026e894ede48d06ff51bc61ae0b9976..34a76c1dff1545480cf801a50a5422b455a77acf 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 96be67a1faa111cebec456d9ea1595c7a2dd0cd9..40fb359484fcbe3116c16024760c014950fab7ca 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_debye_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 244941c117cb1b3aa794406ddc83f3c47da96c70..8c05d14aeffed3d62b66d7cd2a7915e17c61c695 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_dsf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index bcbf7216e2235476dccd02d22b180519a9f10c42..da59873dd20443e141cfa2943769fd8e0def2162 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_long_cs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index fcfb20f3cea076b1449da90a63aaec1fbf166d9b..185d3a7f94d96b6747373f92b0cbda9e0ba93294 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index a2e20d016c8a3a2d0e94718839284cf08b118882..d41be6d8c24b08f11635789d334f4cfde225990e 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_dpd_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index 991c6d900f5ff5f16cb865e2e1ee487224b879db..33d7178faacbea760a25ac7af85fbe7bf72aa456 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_dpd_tstat_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 08ffaef978a5b9bf20023b17a0119639d19a166f..4939537770bee72aafcf0a63b6a5a95c249accc1 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -17,7 +17,7 @@ #include "pair_eam_alloy_gpu.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -29,7 +29,7 @@ #include "neigh_request.h" #include "gpu_extra.h" #include "domain.h" -#include "utils.h" + #include "suffix.h" #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index a82107749b17c6a60908273fba481435724eda01..eb028bc778b744e989dbf2d49b5495af3717a5bb 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -17,7 +17,7 @@ #include "pair_eam_fs_gpu.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -30,7 +30,7 @@ #include "gpu_extra.h" #include "domain.h" #include "suffix.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index 1aac379c35b3057a37d70478aadb6e3b006eb139..3965f27c675e70e562c22336d881cdfd23aad21e 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_eam_gpu.h" #include #include -#include + #include #include "atom.h" #include "force.h" diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index eb83d5af441ec2e20cb37b84250a26fdadfdcf3b..51d4851dc5a91cee4be1804562dc27d220aab1ab 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_gauss_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 83b24f87744a2b50bbf1bb9d3269a10a60c1a7e0..451799027baf4ea972d5570213c810c9d04a2272 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_gayberne_gpu.h" #include #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 7b0d45a43770ce812e620841a7360669c0094ce6..215998bc88a3727fd67141da31bfad8c8d206824 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj96_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index b08ad5e2329b3e77af5cdaefde0171126f5b864a..09ed178200bda130aa8989f29ed0ee727a8f65c8 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_charmm_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index 46ecaea9b8b69acc12b6118fe1cf3447d1c708e7..f6d671d95a86461a23c2b7711cf6b7c04ff9e49c 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_class2_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index a7ca661927c1757a4001f5d13c8b648677a3813d..fbd6aea08cd10702459b2be8f45532763b225e67 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_class2_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 38f6e1f908ae7fe810c35cc6156c84f762cd63c1..28e74d8f396a30c3171551fa168e97bf32bfcc80 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cubic_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index 54f0e92bd50fd1cbd05d59aa34952251aa3a0673..48770d27131ab838b7cddfde3ce645bcc89d30b6 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index e7b1ac5002d72e1d66ae0690eff8f860543a82a2..45c3cc82a0c9a5b32823c38e5ee981c2ebd31f9f 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_debye_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index 5d1f4f70bef08121779d0f282760bf68101b9604..784c0e379d3eac339a4dcce04e6166e987fa27e6 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_dsf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index dff2ba28d47eca5a75b0c7583b6cdfbf5e9f2c25..2a9d431a427ac9ec1a8ab6d6179b5a506089ecfd 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 2f965d6476ac08c2e01bd3147e10aa9259523144..f5987c0ddfc94a968965081674714c065fd63f9a 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_coul_msm_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 43c2a1e9b7d02792e08f88790c984ac6dc1f23f4..ac053037d80ac665e73c5442e2c6bf3b11019bac 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_dipole_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 9416ede51670c2662ad889838f5de240969567b8..7de9ae2aa69bce4eff8458709014511db3326a26 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_dipole_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index 27924361f228b3ca9a1c966c2398a7d7e7053aca..5656c2e18d17c79477a83a1f4b9f5f00b3d454e4 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp index 7c1bb74158480fda3b3807072b057f89b5fe82fa..2bd7420e72b83fe2aad96d45a7c9ab7fe7cdf63d 100644 --- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_lj_cut_tip4p_long_gpu.h" #include "atom.h" diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 54eb4d47e6babe2232083933f388ec20b8cb4339..f13eea51e75c2ee72a7545ad0d508852ed1d8b09 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_expand_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index 32c35420a22cd64f17235cc3f28b3e96d5243b36..bdfa30b9651b770cfab24fbc7bd1a54991d163c6 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_expand_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index d7122cb5f3c6bf5821732c20851d0421f02df244..6d6abdb40d66b5f8e4e8b27a16696f1cb598ee5f 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_gromacs_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index cd76bbd2e9cd87c184517ee4181f9b8f8bb22f8b..4054f08523c7bd85abc9dc2d4794cc6efce7c9ba 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sdk_coul_long_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 5f07bdbb6c1334e23c0fa74f7f92f9404f7db2d2..2016d1db2cc9cda04087e542c1a5faf84fcb512b 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sdk_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index a9ddf81bf094371e54d8d36fbd73e35a21b03e6a..e6834298f374f0a5ea31cd20c27cc1323111e82e 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_lj_sf_dipole_sf_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 4db07ab79e53ed070b54584e1a4aa5679625e0c5..60e6e935e85355109f73de8ea6e61655259b4830 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_mie_cut_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index fc966f6533784054e30d6c7b28cd5b9ae5115a6e..a256f500ceed0451dee936381dcad68b1297376e 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_morse_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 0bcabb451c8920f3c6505359f49d60575e66788d..ca70e3c3377c314c448ef266b74ef18bc945faed 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_resquared_gpu.h" #include #include -#include + #include #include "math_extra.h" #include "atom.h" diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index 48a4f689ff2a84e352ca2c856d857540b12950e8..49c27f515df58cc5ed764628afda55427a33e4c3 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_soft_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 4c4502828d56f171a76c24d5f437e6a5f7046a76..d544534c9d72bc1f02bb7a7dd67b641e09f39c32 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_sw_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index 858a2107dc211d80152f26ff9190107ae6c4b2e2..4ac674aa94ce5aa2a4ac85af431fb26c25dce964 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_table_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index d7b1ef5dd50c18c7ec7951e2fdbf8188dd79f9fd..885dd73d9ed67392610f847e7fee2b66d5603765 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index 1b3504590284c98c7350f6203df4e8d7c21c70ce..35edd9ea220d064b2debc801a63e116a87fe6329 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_mod_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index ae50552f149dcfb4cd0f1e1d2145e0339b2ce10e..73251ee726f2a9b23a6a573562b69a32f0fb1497 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_tersoff_zbl_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 2b4cc2269f4bfe0035d6aa9a36edb7c59221bcbb..fe6adfef12b5618b65dba3442857bb6031281f3f 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -20,7 +20,7 @@ #include "pair_ufm_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index ccd277313016e82b2cc9bf9e5be4fa059bb1f721..868b8de0c0e2528d107a63af3a0ffb32ca2e80aa 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_vashishta_gpu.h" #include #include -#include + #include #include "atom.h" #include "neighbor.h" diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index c3439e3306b07b1f6a833895cf977802d547bd17..3c7b2f5ba7dd9868590e7307bcc8cefeea1be94c 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_yukawa_colloid_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index b9b9d6e0a49751bacaab9f99466680fd3db04277..8147609f45d12ee2a2e926b577407792b30c6ab0 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -18,7 +18,7 @@ #include "pair_yukawa_gpu.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index d0cbfa1d7c30646c9ab769f491f4ebaa9090af9f..0472d9b7c10f1b60f5a1e3558bbc208fd458d371 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -19,7 +19,7 @@ #include "lmptype.h" #include #include -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp index 1df5c9d0a8e945ea17ed51bd7deb95a3b6e3c9dd..dd68aa032f3d437b499e6d8db6977cf1519c874c 100644 --- a/src/GRANULAR/fix_freeze.cpp +++ b/src/GRANULAR/fix_freeze.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_freeze.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp index 879f48e023963d250d19d35745d7fa8332a93261..d449bb5614fa04f15991deb1e20a93bcbb06b393 100644 --- a/src/GRANULAR/fix_pour.cpp +++ b/src/GRANULAR/fix_pour.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_pour.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index a8cd808411610fa106881d11438ebb138c2b9665..68a7803f4bf62cb9726b7b9c139e11cb27649156 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_gran_hooke_history.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 88a9fe36f074b274a270d57c1c8466c09f27fbe0..ee0eb2ad774fe655f0d1d7556a456a38b5d26ff1 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -18,10 +18,10 @@ ----------------------------------------------------------------------- */ #include "pair_granular.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -37,7 +37,7 @@ #include "error.h" #include "math_const.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KIM/kim_init.cpp b/src/KIM/kim_init.cpp index 5e3bd934a95156f9bf26264c87f9211817e5acea..684108be715363b2dddee3ea37611dc27419ffd4 100644 --- a/src/KIM/kim_init.cpp +++ b/src/KIM/kim_init.cpp @@ -57,24 +57,19 @@ ------------------------------------------------------------------------- */ #include "kim_init.h" -#include "fix_store_kim.h" -#include "kim_units.h" -#include -#include -#include -#include -#include "error.h" -#include "atom.h" + +#include "citeme.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix_store_kim.h" +#include "input.h" +#include "kim_units.h" #include "modify.h" -#include "update.h" #include "universe.h" -#include "input.h" #include "variable.h" -#include "citeme.h" -#include "utils.h" -#include "fmt/format.h" + +#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KIM/kim_init.h b/src/KIM/kim_init.h index 3311d4e13d2c45aa8a05a772c9a773bd7a17184f..8fa3247b228d4314f0e5f89613af90c0645030ba 100644 --- a/src/KIM/kim_init.h +++ b/src/KIM/kim_init.h @@ -66,7 +66,6 @@ CommandStyle(kim_init,KimInit) #define LMP_KIM_INIT_H #include "pointers.h" -#include // Forward declaration. typedef struct KIM_Model KIM_Model; diff --git a/src/KIM/kim_interactions.cpp b/src/KIM/kim_interactions.cpp index a91c615d09716f432fbec56cc01915f85cade4be..5f45dd34dc341672437f04039e375ab67e8f59de 100644 --- a/src/KIM/kim_interactions.cpp +++ b/src/KIM/kim_interactions.cpp @@ -57,23 +57,18 @@ ------------------------------------------------------------------------- */ #include "kim_interactions.h" -#include -#include -#include -#include -#include -#include "error.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix_store_kim.h" +#include "input.h" #include "modify.h" #include "update.h" -#include "universe.h" -#include "input.h" -#include "variable.h" -#include "utils.h" -#include "fix_store_kim.h" -#include "fmt/format.h" + +#include +#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KIM/kim_interactions.h b/src/KIM/kim_interactions.h index 414c7b39d5f3684acd563dce8e17f6ecf207c8bf..071e5b284faaa9edb9317bde06cc6ea31c56540d 100644 --- a/src/KIM/kim_interactions.h +++ b/src/KIM/kim_interactions.h @@ -66,7 +66,6 @@ CommandStyle(kim_interactions,KimInteractions) #define LMP_KIM_INTERACTIONS_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_param.cpp b/src/KIM/kim_param.cpp index 6df8c075dc7dd3069256a6494059e4911e902d29..6f4ac5cc21e1f98554f717017099fe282cb5665e 100644 --- a/src/KIM/kim_param.cpp +++ b/src/KIM/kim_param.cpp @@ -56,19 +56,17 @@ ------------------------------------------------------------------------- */ #include "kim_param.h" -#include "fix_store_kim.h" -#include "pair_kim.h" -#include -#include -#include -#include -#include "comm.h" + #include "error.h" +#include "fix_store_kim.h" +#include "force.h" #include "input.h" #include "modify.h" +#include "pair_kim.h" #include "variable.h" -#include "force.h" -#include "fmt/format.h" + +#include +#include extern "C" { diff --git a/src/KIM/kim_param.h b/src/KIM/kim_param.h index a4e26451f2b55b67876aabe45f309d04f4cdd9e9..e4fc5ce59a96ba4593ac0a87af297c10bc8ff0bb 100644 --- a/src/KIM/kim_param.h +++ b/src/KIM/kim_param.h @@ -65,7 +65,6 @@ CommandStyle(kim_param, KimParam) #define LMP_KIM_PARAM_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_property.cpp b/src/KIM/kim_property.cpp index 643e0da47b95e953e4265b0ec69e8bedb27ebe96..95a12748596609d99fc179fe9458919fea1cd11e 100644 --- a/src/KIM/kim_property.cpp +++ b/src/KIM/kim_property.cpp @@ -53,21 +53,18 @@ Designed for use with the kim-api-2.1.0 (and newer) package ------------------------------------------------------------------------- */ -#if LMP_PYTHON -#define PY_SSIZE_T_CLEAN -#include -#endif - #include "kim_property.h" #include "comm.h" -#include "input.h" -#include "variable.h" -#include "utils.h" #include "error.h" +#include "input.h" #include "lmppython.h" +#include "variable.h" -#include +#if LMP_PYTHON +#define PY_SSIZE_T_CLEAN +#include // IWYU pragma: export +#endif using namespace LAMMPS_NS; diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp index 4a1db9450d96fdf696fe0ca0ab2ddfc4f6b9b540..ec13210665cf897e09f1de018d49b06ca04fafdc 100644 --- a/src/KIM/kim_query.cpp +++ b/src/KIM/kim_query.cpp @@ -56,24 +56,22 @@ ------------------------------------------------------------------------- */ #include "kim_query.h" -#include "fix_store_kim.h" -#include -#include -#include -#include + #include "comm.h" #include "error.h" +#include "fix_store_kim.h" +#include "info.h" #include "input.h" #include "modify.h" #include "variable.h" #include "version.h" -#include "info.h" -#include "fmt/format.h" + +#include +#include #if defined(LMP_KIM_CURL) #include #include -#include #endif using namespace LAMMPS_NS; diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h index 6888f911f4baae98473398d930e079137dddac7f..e1c49ed71d33c3f5d9cd73685d52a7cd23323cdd 100644 --- a/src/KIM/kim_query.h +++ b/src/KIM/kim_query.h @@ -64,7 +64,6 @@ CommandStyle(kim_query,KimQuery) #define LMP_KIM_QUERY_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/KIM/kim_units.cpp b/src/KIM/kim_units.cpp index c0c1aee07c9d554410404b00f9dcc9b93c20f3c8..77dbad6f1d20e7cb66e975262d19db7836432e2e 100644 --- a/src/KIM/kim_units.cpp +++ b/src/KIM/kim_units.cpp @@ -57,6 +57,8 @@ #include #include #include +#include + using namespace std; namespace diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index 69586b55d62feab5bae167b907b44212ee88dbcd..7ed70972c5060cad0c7f00e08a6594e9d4637634 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -55,21 +55,20 @@ Designed for use with the kim-api-2.0.2 (and newer) package ------------------------------------------------------------------------- */ #include "pair_kim.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "update.h" -#include "memory.h" -#include "domain.h" -#include "utils.h" -#include "error.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index 1f2c8c8599f57f6808ce610664b332952ab52562..0c2e8d2684ca1bd1275811430745772f8381808b 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -65,7 +65,6 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" -#include extern "C" { #include "KIM_SimulatorHeaders.h" diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 288e5a475b1e97c5c53018d643b04b2239e5fe5e..59ccac92cef7821f758863165fa5249e42ae85d4 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_charmm_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index ebb016b31bd78fda5469aea2666319295ff28c5b..bfa0f81a1df521de4d1ac183b324a7499caa8b9e 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_class2_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp index 960988b3b50d7c7392f66e9797f5f2a5af133a3e..cf93bfbde50d16a3c93154f51dd2a54fa2386637 100644 --- a/src/KOKKOS/angle_cosine_kokkos.cpp +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index bc08ff4b6554feb7f4b93eef924b8ab02c4c857f..3a8878d222057f2e23dc310c3acc5c7db80cead7 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index ce480f6f9d26d6bb9ccb49f133b995cd8471844f..6eebbad661bd8c89494f4a1960cf99fda6dba2ff 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "atom.h" +#include "atom.h" // IWYU pragma: export #include "kokkos_type.h" #ifndef LMP_ATOM_KOKKOS_H diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp index e9fee6d8f6a9d3a0a8bd07acf0d2913e2f0ef1a8..662f09fe5a008b7d171d81634a35001d41657644 100644 --- a/src/KOKKOS/atom_vec_angle_kokkos.cpp +++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_angle_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" -#include "utils.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp index 7a66dc753a88fac40b50415ece5a8059684f8fe7..995985b29df4ff14bc4763b364f0ca4b3ae3f267 100644 --- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp +++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_atomic_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" -#include "utils.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp index 157f194125ed889c7a2b694dd00c846560b68e93..db56d58dffbac5ba982548555787459cbdeeb3c4 100644 --- a/src/KOKKOS/atom_vec_bond_kokkos.cpp +++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_bond_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" -#include "utils.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp index 8f468b8e46ebd52b7d0b1a097061ae1c6b11c253..9846d2f4f83541088bbee94a8a855450ce6ddcc2 100644 --- a/src/KOKKOS/atom_vec_charge_kokkos.cpp +++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_charge_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" -#include "utils.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp index 5319744c22405304c6e44254d56aa40034faaf70..b112605859853af7f94be334915f523027798da2 100644 --- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp +++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp index 5d5833af07079545dcc960b42375fa62019124db..89275c70674047a2aef8565ac80ef92d03070c71 100644 --- a/src/KOKKOS/atom_vec_full_kokkos.cpp +++ b/src/KOKKOS/atom_vec_full_kokkos.cpp @@ -20,7 +20,7 @@ #include "atom_masks.h" #include "memory_kokkos.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp index 0cc609f91cc8a3aaef13571fb2dfe232ee3d4f01..7c7f3c98260b4325f6c6f4fe287f49aa6a3019c8 100644 --- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp +++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid_kokkos.h" -#include + #include "atom_kokkos.h" +#include "atom_masks.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "utils.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; @@ -1177,7 +1178,7 @@ void AtomVecHybridKokkos::build_styles() allstyles[nallstyles] = new char[n]; \ strcpy(allstyles[nallstyles],#key); \ nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS } diff --git a/src/KOKKOS/atom_vec_kokkos.cpp b/src/KOKKOS/atom_vec_kokkos.cpp index b0fca4e316637cc67f8556ebd3edd2b13732bb8f..9e39f537335843430b897063468c5b8a546c5d82 100644 --- a/src/KOKKOS/atom_vec_kokkos.cpp +++ b/src/KOKKOS/atom_vec_kokkos.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "atom_masks.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index 7d8796b1ae18bc34e649279be0993f0053d6c63f..d414101966d1626a0efc807c61c17c38544f6e85 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -14,7 +14,8 @@ #ifndef LMP_ATOM_VEC_KOKKOS_H #define LMP_ATOM_VEC_KOKKOS_H -#include "atom_vec.h" +#include "atom_vec.h" // IWYU pragma: export + #include "kokkos_type.h" #include diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp index 7832d6f9b0eb43dcbd907120f2b72ffaf414721d..7e3cdbf5e3d572930434520ba036cf86afd6f3bb 100644 --- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp +++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_molecular_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" #include "memory_kokkos.h" -#include "error.h" -#include "utils.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index b1099d0fa6e4c5e61211f71dfda060e6bf627fff..6b62014e4ad3c570789f4ff998b7952af40e52bb 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -12,27 +12,26 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere_kokkos.h" -#include -#include + #include "atom_kokkos.h" #include "atom_masks.h" #include "comm_kokkos.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" #include "memory.h" -#include "error.h" #include "memory_kokkos.h" -#include "utils.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; +using namespace MathConst; #define DELTA 10 -static const double MY_PI = 3.14159265358979323846; // pi - /* ---------------------------------------------------------------------- */ AtomVecSphereKokkos::AtomVecSphereKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index 88504608f636d434ea2e273a847605c6c81f4ae6..07712df203c5b84328b36b73db15cd7e59718c52 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -16,16 +16,15 @@ ------------------------------------------------------------------------- */ #include "bond_class2_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index e6aa27649fff4a51a216b8b7f2af906937a3dd6d..1ee82476b2907ac6d6ea6deafb45f56efc72b420 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "bond_fene_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index ee1b58c91fb92abab8dc1e4a4bb727b7387737ac..20b87784638a9766d56199dbb167ad833aeaf3a0 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -16,19 +16,17 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "force.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" -using namespace LAMMPS_NS; +#include +using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index 8f865f64592357725d556f84350d03eb292c224e..51ba6bbdb240b776c0e1011cb24538fba905df78 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -12,23 +12,24 @@ ------------------------------------------------------------------------- */ #include "comm_kokkos.h" -#include "kokkos.h" + #include "atom.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" #include "atom_vec_kokkos.h" +#include "compute.h" #include "domain.h" -#include "atom_masks.h" +#include "dump.h" #include "error.h" -#include "memory_kokkos.h" -#include "force.h" -#include "pair.h" #include "fix.h" -#include "compute.h" -#include "dump.h" -#include "output.h" -#include "modify.h" +#include "force.h" +#include "kokkos.h" #include "kokkos_base.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "output.h" +#include "pair.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp index a29d9f63b391b25798fd48ff825f481d86ddc15e..88d3d1ac8c20dfd51a79a5e46d7e0b9ebc2a6870 100644 --- a/src/KOKKOS/comm_tiled_kokkos.cpp +++ b/src/KOKKOS/comm_tiled_kokkos.cpp @@ -12,22 +12,10 @@ ------------------------------------------------------------------------- */ #include "comm_tiled_kokkos.h" -#include -#include "comm_brick.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "domain.h" -#include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" -#include "output.h" -#include "dump.h" -#include "memory_kokkos.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/compute_coord_atom_kokkos.cpp b/src/KOKKOS/compute_coord_atom_kokkos.cpp index 90bd151b2d6eb00bd4d4b46878d4324852a43c85..c1f9324942817f1728e0ec959b3c63335fb07d90 100644 --- a/src/KOKKOS/compute_coord_atom_kokkos.cpp +++ b/src/KOKKOS/compute_coord_atom_kokkos.cpp @@ -12,22 +12,18 @@ ------------------------------------------------------------------------- */ #include "compute_coord_atom_kokkos.h" -#include -#include -#include "compute_orientorder_atom_kokkos.h" + #include "atom_kokkos.h" -#include "update.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute_orientorder_atom_kokkos.h" +#include "error.h" +#include "memory_kokkos.h" #include "modify.h" -#include "neighbor_kokkos.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" -#include "group.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp index b17434d09abda47df7d1fcec3024b66ccff3c735..6e35dfd94f61d41f3882bd2cee22511958cad296 100644 --- a/src/KOKKOS/compute_orientorder_atom_kokkos.cpp +++ b/src/KOKKOS/compute_orientorder_atom_kokkos.cpp @@ -16,23 +16,19 @@ ------------------------------------------------------------------------- */ #include "compute_orientorder_atom_kokkos.h" -#include -#include -#include + #include "atom_kokkos.h" -#include "update.h" -#include "modify.h" -#include "neighbor_kokkos.h" +#include "atom_masks.h" +#include "kokkos.h" +#include "math_const.h" +#include "memory_kokkos.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor_kokkos.h" #include "pair.h" -#include "comm.h" -#include "memory_kokkos.h" -#include "error.h" -#include "math_const.h" -#include "atom_masks.h" -#include "kokkos.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index 0e7fe255402ea9dcf99cf8193608383880fc97dd..5e60d62be1cf3f0b14a26e9f4a4e4f21ab18ae19 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -12,16 +12,15 @@ ------------------------------------------------------------------------- */ #include "compute_temp_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "update.h" -#include "force.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" -#include "group.h" #include "error.h" -#include "atom_masks.h" +#include "force.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 0d8256f306ac778b188f0a0025b3ac0411ee6044..88b5e1344d8272617fc03d22789c76fe4a6c6a20 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -16,19 +16,18 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmm_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "atom_masks.h" +#include "error.h" #include "force.h" -#include "pair.h" +#include "kokkos.h" #include "math_const.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" -#include "kokkos.h" +#include "neighbor_kokkos.h" +#include "pair.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index 371af44e9a8d4c6e2fcc306996762659f27111b2..156a13c2ecd81b0dd97f127f879eaf7627bc8677 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_class2_kokkos.h" -#include -#include + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_harmonic_kokkos.cpp b/src/KOKKOS/dihedral_harmonic_kokkos.cpp index 408fa276e4a64235ea0d8eea55509a05032028dc..d4855b10c1c6807eda335b3a138bac4216504619 100644 --- a/src/KOKKOS/dihedral_harmonic_kokkos.cpp +++ b/src/KOKKOS/dihedral_harmonic_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_harmonic_kokkos.h" -#include -#include + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 309d617f0ab3023a0060eca7695cf306c1bbe07f..42874936f932d81eac05d38afcf5383d7a6d26b4 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls_kokkos.h" -#include -#include + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor_kokkos.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neighbor_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/domain_kokkos.h b/src/KOKKOS/domain_kokkos.h index eccc36a021ec5bc90a8ce3f838b2f9625c78b42b..3bfdeb708b7aebba720bbdcc51e339306d0d7d47 100644 --- a/src/KOKKOS/domain_kokkos.h +++ b/src/KOKKOS/domain_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_DOMAIN_KOKKOS_H #define LMP_DOMAIN_KOKKOS_H -#include "domain.h" +#include "domain.h" // IWYU pragma: export #include "kokkos_type.h" #include "kokkos_few.h" diff --git a/src/KOKKOS/fft3d_kokkos.cpp b/src/KOKKOS/fft3d_kokkos.cpp index e49d780040b6bf34bedb286087918d94a0fa4c4a..ff95998e4ec7a98241e9a19c4c1c11995306ba24 100644 --- a/src/KOKKOS/fft3d_kokkos.cpp +++ b/src/KOKKOS/fft3d_kokkos.cpp @@ -14,16 +14,13 @@ /* ---------------------------------------------------------------------- Contributing authors: Stan Moore (SNL), Sam Mish (U.C. Davis) ------------------------------------------------------------------------- */ - -#include -#include -#include -#include #include "fft3d_kokkos.h" -#include "remap_kokkos.h" + #include "error.h" #include "kokkos.h" +#include "remap_kokkos.h" +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp index 05eb1c22f66a3af0545dacb94ad114732705a2b6..87d860b5ae8747c04bd68c0e4894225e7872d177 100644 --- a/src/KOKKOS/fix_deform_kokkos.cpp +++ b/src/KOKKOS/fix_deform_kokkos.cpp @@ -16,23 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_deform_kokkos.h" -#include -#include -#include + #include "atom_kokkos.h" -#include "update.h" -#include "comm.h" -#include "irregular.h" +#include "atom_masks.h" #include "domain_kokkos.h" -#include "lattice.h" +#include "error.h" #include "force.h" -#include "modify.h" -#include "math_const.h" -#include "kspace.h" #include "input.h" +#include "irregular.h" +#include "kspace.h" +#include "math_const.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "atom_masks.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_gravity_kokkos.cpp b/src/KOKKOS/fix_gravity_kokkos.cpp index 4f8b57365e72eb76805b55c81466ec1f1e96c66e..7d413a1d5797ffa2fc831b2e26f9dd4011c64f5a 100644 --- a/src/KOKKOS/fix_gravity_kokkos.cpp +++ b/src/KOKKOS/fix_gravity_kokkos.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_gravity_kokkos.h" + +#include "atom_kokkos.h" #include "atom_masks.h" -#include "modify.h" +#include "atom_vec.h" #include "input.h" -#include "variable.h" +#include "modify.h" #include "update.h" -#include "atom_kokkos.h" -#include "atom_vec.h" +#include "variable.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 44ae18f9a9bbd692aad90033b370c0b37eab0cf3..dadf9e4c8b3adf2b6468b9a4cc4d253ba0b25bac 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -12,21 +12,22 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_kokkos.h" -#include -#include "atom_masks.h" + #include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm.h" +#include "compute.h" +#include "error.h" #include "force.h" #include "group.h" -#include "update.h" -#include "error.h" +#include "input.h" #include "memory_kokkos.h" -#include "compute.h" -#include "comm.h" #include "modify.h" -#include "input.h" -#include "region.h" +#include "update.h" #include "variable.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_minimize_kokkos.cpp b/src/KOKKOS/fix_minimize_kokkos.cpp index e7b10dbb8eae2c90a0593fd590fbaf028eb73fe9..13b9cb02a735fdf753b56cb3f3c3b7c95b3d28ef 100644 --- a/src/KOKKOS/fix_minimize_kokkos.cpp +++ b/src/KOKKOS/fix_minimize_kokkos.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_minimize_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "domain.h" #include "memory_kokkos.h" -#include "atom_masks.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 9c9d6cb1cddf9de3efb15d648ee95f819b52042e..be486bf752c9c8aacafcdf778a83b3a80ec4aeba 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "fix_momentum_kokkos.h" -#include -#include + #include "atom_kokkos.h" #include "atom_masks.h" -#include "domain.h" #include "domain_kokkos.h" #include "group.h" #include "error.h" -#include "force.h" #include "kokkos_few.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index a43c5ef458bff9122741d7c4ad5786eb42bd8b3a..d1f3f6632766b5f9a31b27cb42edf59f7a1264c5 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_neigh_history_kokkos.h" + #include "atom_kokkos.h" #include "error.h" #include "memory_kokkos.h" +#include "modify.h" #include "neigh_list_kokkos.h" #include "pair_kokkos.h" -#include "comm.h" -#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 96e966371225f636ab1a021f6788b834b53d75a0..a2985502bb0e5c57ad904e98ec89a704a5e834b3 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -16,27 +16,24 @@ ------------------------------------------------------------------------- */ #include "fix_nh_kokkos.h" -#include -#include -#include -#include "math_extra.h" + #include "atom.h" -#include "force.h" -#include "group.h" +#include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" -#include "neighbor.h" -#include "irregular.h" -#include "modify.h" -#include "fix_deform.h" #include "compute.h" -#include "kspace.h" -#include "update.h" -#include "respa.h" #include "domain_kokkos.h" -#include "memory_kokkos.h" #include "error.h" -#include "atom_masks.h" -#include "atom_kokkos.h" +#include "fix_deform.h" +#include "force.h" +#include "irregular.h" +#include "kspace.h" +#include "memory_kokkos.h" +#include "neighbor.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index d667e29221f4fb0ee9048b8f6323994ae63fa10f..7efcb150bd00193330c244b66c1b3a3a5877ca44 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nph_kokkos.h" -#include + #include "modify.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index 47b3da4efe21f8760a1df2d8ae8e7e6425cb142e..5b73eee4d71e8f0660420dc1307c6d32976668d6 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_npt_kokkos.h" -#include + #include "modify.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index da0a326d5d3a14428f748bea323dadac4f32dd85..beabc5572728bbd78c97728a45548cd3ff571cb0 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_nve_kokkos.h" -#include -#include -#include "atom_masks.h" + #include "atom_kokkos.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" +#include "atom_masks.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 013095abc0321f483dceb4d802294b79267bdfef..6e6958261705150fe473ab05d3cc145547e89eb5 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -12,10 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_nvt_kokkos.h" -#include + +#include "error.h" #include "group.h" #include "modify.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp index ff374b885f909de1bc163343fcfc80671bf3b5e5..185e7445b22afc8adbae2cde835c8e786aab6d1c 100644 --- a/src/KOKKOS/fix_property_atom_kokkos.cpp +++ b/src/KOKKOS/fix_property_atom_kokkos.cpp @@ -12,14 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_property_atom_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "comm.h" -#include "memory_kokkos.h" -#include "error.h" -#include "update.h" #include "atom_masks.h" +#include "error.h" +#include "memory_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 8c007586a910049ca77576624eaca252f0bb559d..eac044da28bf15db65af63f492e05473bc5b8ebc 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -17,21 +17,21 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax_kokkos.h" -#include -#include "kokkos.h" + #include "atom.h" -#include "atom_masks.h" #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "kokkos.h" +#include "memory_kokkos.h" #include "neigh_list_kokkos.h" #include "neigh_request.h" +#include "neighbor.h" #include "update.h" -#include "integrate.h" -#include "memory_kokkos.h" -#include "error.h" -#include "pair_reaxc_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp index 3a706ece83c1c26bfe4d99bd13b5f4b7f44d9837..f98ab0314cf6ba5d679614730dafe71062374842 100644 --- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp +++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_bonds_kokkos.h" + #include "atom.h" -#include "pair_reaxc_kokkos.h" +#include "atom_masks.h" +#include "error.h" #include "force.h" -#include "compute.h" #include "memory_kokkos.h" -#include "error.h" -#include "reaxc_defs.h" -#include "atom_masks.h" +#include "pair_reaxc_kokkos.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index 38968bdd3561b212a2b407b40388b402f88b23ae..18bc4225a70c640cb70d9b37fbf7b46ea436fba9 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -27,7 +27,7 @@ #include "comm.h" #include "domain.h" #include "kokkos.h" -#include "utils.h" + #include // DBL_EPSILON diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index da516f5ba20c143fe1b177d79b46cea669cc87cd..a11e8b4bd4d32d642dd15071b32e1ce643d30d35 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_setforce_kokkos.h" -#include + #include "atom_kokkos.h" #include "update.h" #include "modify.h" @@ -24,7 +24,8 @@ #include "error.h" #include "atom_masks.h" #include "kokkos_base.h" -#include "region.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 75964f48296914e90f33f197b3e021aae5795120..9be4321ff2dc0f8f70f4bf56fed6e666780d71d0 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -35,7 +35,7 @@ #include "fix_shardlow_kokkos.h" #include -#include + #include "atom.h" #include "atom_masks.h" #include "atom_kokkos.h" diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index a5bd6e6e6c1cb7128ef7792ec966063e483389cf..046c97c12bd3657950701f5b99e2a1dfc9e61b2d 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -12,20 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "comm.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" +#include "atom_masks.h" #include "input.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" -#include "atom_masks.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 5f32c5b4aec3ea7de7ce02b152768272a7cd4192..909e3c8544c7ea1fac299e7e5526c0379e194c62 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -12,14 +12,13 @@ ------------------------------------------------------------------------- */ #include "gridcomm_kokkos.h" -#include + #include "comm.h" -#include "kspace.h" #include "irregular.h" -#include "memory_kokkos.h" -#include "error.h" -#include "kokkos_base_fft.h" #include "kokkos.h" +#include "kokkos_base_fft.h" +#include "kspace.h" +#include "memory_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index b5e617452884c11ec6409749899c97cc77bf202f..79fd0685b079c5cd901133d90b7bc79dc84f0529 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -12,19 +12,17 @@ ------------------------------------------------------------------------- */ #include "kokkos.h" -#include -#include + +#include "error.h" +#include "force.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neighbor_kokkos.h" + #include -#include #include #include #include -#include "lammps.h" -#include "force.h" -#include "neighbor_kokkos.h" -#include "neigh_list_kokkos.h" -#include "error.h" -#include "memory_kokkos.h" #ifdef KOKKOS_ENABLE_CUDA diff --git a/src/KOKKOS/memory_kokkos.h b/src/KOKKOS/memory_kokkos.h index 39d30ac78540c66724d8a00f0a1a9eff9687416a..83e8b9ec7cd02faff17d9fea767df9eeaf7b79e7 100644 --- a/src/KOKKOS/memory_kokkos.h +++ b/src/KOKKOS/memory_kokkos.h @@ -14,7 +14,7 @@ #ifndef LMP_MEMORY_KOKKOS_H #define LMP_MEMORY_KOKKOS_H -#include "memory.h" +#include "memory.h" // IWYU pragma: export #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/min_kokkos.cpp b/src/KOKKOS/min_kokkos.cpp index e5f22411f60fb2f4affee20e0df3f49f80101eef..032538fe601a8f63ce197582af0232b88f5c9a49 100644 --- a/src/KOKKOS/min_kokkos.cpp +++ b/src/KOKKOS/min_kokkos.cpp @@ -16,32 +16,31 @@ ------------------------------------------------------------------------- */ #include "min_kokkos.h" -#include -#include -#include + +#include "angle.h" #include "atom_kokkos.h" -#include "atom_vec.h" -#include "domain.h" +#include "atom_masks.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" -#include "fix_minimize_kokkos.h" #include "compute.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_minimize_kokkos.h" +#include "force.h" #include "improper.h" +#include "kokkos.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "kokkos.h" -#include "atom_masks.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/min_linesearch_kokkos.cpp b/src/KOKKOS/min_linesearch_kokkos.cpp index cb07c7db86e805241a75e455b84ff349977ed717..4306a5bd3b4bac5cb162eb651b0ea9c9dfb5c434 100644 --- a/src/KOKKOS/min_linesearch_kokkos.cpp +++ b/src/KOKKOS/min_linesearch_kokkos.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "min_linesearch_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "modify.h" +#include "atom_masks.h" +#include "error.h" #include "fix_minimize_kokkos.h" -#include "pair.h" #include "output.h" +#include "pair.h" #include "thermo.h" -#include "error.h" -#include "atom_masks.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp index 89a69dc6331d2314cc8af699d06f32a2d9803076..158a87796ee46896de0a3c67f0af22b9c9a5a37d 100644 --- a/src/KOKKOS/nbin_kokkos.cpp +++ b/src/KOKKOS/nbin_kokkos.cpp @@ -12,14 +12,11 @@ ------------------------------------------------------------------------- */ #include "nbin_kokkos.h" -#include "neighbor.h" + #include "atom_kokkos.h" -#include "group.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" #include "update.h" -#include "error.h" -#include "atom_masks.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index bf9234e17c1fe61be7f5aecfe27b2dc36572af16..021dcc7a1c1ae6769344ddcff1e339f97365d9c3 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -16,22 +16,22 @@ ------------------------------------------------------------------------- */ #include "neigh_bond_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "update.h" #include "domain_kokkos.h" -#include "output.h" -#include "thermo.h" -#include "memory_kokkos.h" #include "error.h" -#include "modify.h" #include "fix.h" -#include -#include "atom_masks.h" -#include "domain.h" +#include "force.h" +#include "memory_kokkos.h" +#include "modify.h" +#include "output.h" +#include "thermo.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; #define BONDDELTA 10000 diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index 14591f82461c721591d69aa915bec7d22c895156..7db78e38d24255fa98e90003ec1c7b9f4f6200b6 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "neigh_list_kokkos.h" -#include "atom.h" -#include "memory_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h index edd775f7f960b82082b7baabcf31082113d191e2..8ae873036b895cde1de9552c469d827a6b7cee38 100644 --- a/src/KOKKOS/neigh_list_kokkos.h +++ b/src/KOKKOS/neigh_list_kokkos.h @@ -15,7 +15,8 @@ #define LMP_NEIGH_LIST_KOKKOS_H #include "pointers.h" -#include "neigh_list.h" + +#include "neigh_list.h" // IWYU pragma: export #include "kokkos_type.h" namespace LAMMPS_NS { diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp index 4d0cf7ea3a06ca24c6f2baf245ee59a9142ed18f..b21a7cb1ee7e87943bce9aa885ab72b9714bfa98 100644 --- a/src/KOKKOS/neighbor_kokkos.cpp +++ b/src/KOKKOS/neighbor_kokkos.cpp @@ -12,25 +12,26 @@ ------------------------------------------------------------------------- */ #include "neighbor_kokkos.h" + +#include "angle.h" #include "atom_kokkos.h" -#include "pair.h" -#include "fix.h" -#include "neigh_request.h" -#include "memory_kokkos.h" -#include "update.h" #include "atom_masks.h" -#include "error.h" -#include "kokkos.h" -#include "force.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "improper.h" +#include "kokkos.h" +#include "memory_kokkos.h" +#include "neigh_request.h" +#include "pair.h" #include "style_nbin.h" -#include "style_nstencil.h" #include "style_npair.h" +#include "style_nstencil.h" #include "style_ntopo.h" -#include "comm.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h index 3829502c0d967117c350a5ac9eee22014cf7dcd1..304fe8f1da22958b6092e09e277f0de283e151c8 100644 --- a/src/KOKKOS/neighbor_kokkos.h +++ b/src/KOKKOS/neighbor_kokkos.h @@ -14,11 +14,10 @@ #ifndef LMP_NEIGHBOR_KOKKOS_H #define LMP_NEIGHBOR_KOKKOS_H -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: export #include "neigh_list_kokkos.h" #include "neigh_bond_kokkos.h" #include "kokkos_type.h" -#include namespace LAMMPS_NS { diff --git a/src/KOKKOS/npair_halffull_kokkos.cpp b/src/KOKKOS/npair_halffull_kokkos.cpp index b1090109359aa9835302d63c343620c6742519a4..ca9c14b29d1ec3305de524e7133a8d8b7942e71a 100644 --- a/src/KOKKOS/npair_halffull_kokkos.cpp +++ b/src/KOKKOS/npair_halffull_kokkos.cpp @@ -12,15 +12,14 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_kokkos.h" -#include "neighbor.h" -#include "neigh_list_kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "molecule.h" #include "domain.h" -#include "my_page.h" -#include "error.h" -#include "atom_masks.h" +#include "neigh_list_kokkos.h" + +#include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index 13080a9580060307c834d57b893d77a9bace9490..81f78844d317a073d7abee0258c2c25c3ce6713a 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_kokkos.h" -#include "neigh_list_kokkos.h" + #include "atom_kokkos.h" -#include "atom_vec.h" -#include "error.h" #include "atom_masks.h" +#include "atom_vec.h" +#include "neigh_list_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index 28cf65c8d8fd211e91ce0b8643337c52ec292e6a..280e47b77166b9dcdc50b1726a579467c2f3970c 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -29,7 +29,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index da49414892926a5bae4608de7b62f7fedcf7fcdf..a4828c00aa0f245a95d7c45c5980703a265ab7c3 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -29,7 +29,7 @@ #include "memory_kokkos.h" #include "error.h" #include "atom_masks.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index 2e2c3ef04e89f99c2e8e5095f725913653bea469..035bf87cecda8a1d1b7c6955d32fb66f41f25a56 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -17,7 +17,7 @@ #include "pair_exp6_rx_kokkos.h" #include -#include + #include #include "atom.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "neigh_request.h" #include "atom_kokkos.h" #include "kokkos.h" -#include "utils.h" + #ifdef _OPENMP #include diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp index 1f2ad404bb49f9838172291859b9cc90df6eedbd..9c75f3abe8b9ed143e800deeb304ca7866f29bda 100644 --- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -17,7 +17,7 @@ #include "atom.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h index ffafdf7f17f0aed75b62dfbfba1dbb1dd465923d..396a5f2d4872341f7084471ea9df39ea11e1f4bb 100644 --- a/src/KOKKOS/pair_kokkos.h +++ b/src/KOKKOS/pair_kokkos.h @@ -19,7 +19,7 @@ #define LMP_PAIR_KOKKOS_H #include "Kokkos_Macros.hpp" -#include "pair.h" +#include "pair.h" // IWYU pragma: export #include "neighbor_kokkos.h" #include "neigh_list_kokkos.h" #include "Kokkos_Vectorization.hpp" diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index d0fe11285a6ac2c557c4431ec47156c853674da0..3a7359df93feaa357fcf762de3a9c3bfe6f886db 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -16,25 +16,23 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_kokkos.h" -#include -#include -#include -#include "kokkos.h" + #include "atom_kokkos.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list_kokkos.h" +#include "kokkos.h" #include "math_const.h" #include "math_special.h" -#include "memory_kokkos.h" -#include "error.h" -#include "atom_masks.h" +#include "neigh_request.h" +#include "neighbor.h" #include "reaxc_defs.h" #include "reaxc_lookup.h" #include "reaxc_tool_box.h" +#include + #define TEAMSIZE 128 diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 26aa4373ccaa88310fb6b50e36937ef7a0d102c4..09e38e638707bbe552e54f17c4b8950b6b91db0a 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_table_rx_kokkos.h" -#include + #include #include #include "kokkos.h" @@ -33,7 +33,7 @@ #include "kokkos_few.h" #include "kokkos.h" #include "modify.h" -#include "utils.h" + #include using namespace LAMMPS_NS; diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index f5489c0e0c6c463ea870ce242347708205393b0f..b5dd43f12aa3193fd07a1c6c26687d11233d9357 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -16,20 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta_kokkos.h" -#include -#include -#include "kokkos.h" -#include "pair_kokkos.h" + #include "atom_kokkos.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" +#include "atom_masks.h" #include "comm.h" -#include "memory_kokkos.h" -#include "neigh_list_kokkos.h" #include "error.h" -#include "atom_masks.h" +#include "force.h" +#include "kokkos.h" #include "math_const.h" +#include "memory_kokkos.h" +#include "neigh_list_kokkos.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 2eea5279470536e208e8246eeefbafe7ab84202f..4a795833fbf6ffa436df659a4798560ab1acf448 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -16,26 +16,22 @@ ------------------------------------------------------------------------- */ #include "pppm_kokkos.h" -#include -#include + #include "atom_kokkos.h" -#include "comm.h" -#include "gridcomm_kokkos.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" +#include "atom_masks.h" #include "domain.h" -#include "fft3d_kokkos.h" -#include "remap_kokkos.h" -#include "memory_kokkos.h" #include "error.h" -#include "atom_masks.h" +#include "fft3d_kokkos.h" +#include "force.h" +#include "gridcomm_kokkos.h" #include "kokkos.h" -#include "utils.h" -#include "fmt/format.h" - #include "math_const.h" #include "math_special_kokkos.h" +#include "memory_kokkos.h" +#include "pair.h" +#include "remap_kokkos.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KOKKOS/remap_kokkos.cpp b/src/KOKKOS/remap_kokkos.cpp index d496db05e2510cb0509191efbdb2cc9eb6b6eaf7..af87ba3644e1f49c73076f50063688dc5d7efc87 100644 --- a/src/KOKKOS/remap_kokkos.cpp +++ b/src/KOKKOS/remap_kokkos.cpp @@ -11,12 +11,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include #include "remap_kokkos.h" -#include "pack_kokkos.h" + #include "error.h" +#include "pack_kokkos.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index 4aa95318db8ca4d96eb310f59585c55b4fe267b4..6133df398f9abd15b1c94a1453c29a1cdec8defb 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -19,19 +19,17 @@ ------------------------------------------------------------------------- */ #include "ewald.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "pair.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_dipole.cpp b/src/KSPACE/ewald_dipole.cpp index 1921b8dc558f77833ec39722f1a33ea09f7bb57d..33d21b416e7f571dcc27db03da95ef2c267a846c 100644 --- a/src/KSPACE/ewald_dipole.cpp +++ b/src/KSPACE/ewald_dipole.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "ewald_dipole.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_dipole_spin.cpp b/src/KSPACE/ewald_dipole_spin.cpp index bdbb737de8c0a630c7885ad424abb5120ee84081..94cacd3a753d12431ee1a09a8ef586b51cd11b6a 100644 --- a/src/KSPACE/ewald_dipole_spin.cpp +++ b/src/KSPACE/ewald_dipole_spin.cpp @@ -16,21 +16,19 @@ ------------------------------------------------------------------------- */ #include "ewald_dipole_spin.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index b616b2ae5d692fce3f9d2c9ce7cbbbbdf424e047..546ac472c907b7fd7d8defa17519ab5dba3015a1 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -16,23 +16,21 @@ ------------------------------------------------------------------------- */ #include "ewald_disp.h" -#include -#include -#include -#include -#include "math_vector.h" -#include "math_const.h" -#include "math_special.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "math_const.h" +#include "math_special.h" +#include "math_vector.h" +#include "memory.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/fft3d_wrap.cpp b/src/KSPACE/fft3d_wrap.cpp index 507b23d27d9ca7fd1ec83431dfeda6e82f70bbb8..d0e3a2b50c62c6288255582f29ca2a3cf82c45cf 100644 --- a/src/KSPACE/fft3d_wrap.cpp +++ b/src/KSPACE/fft3d_wrap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fft3d_wrap.h" -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index 45c8a359711f39ae1fa877698f0d0341ece1db8d..c205f9de05fc82710392a5790bcf477e4d57bcc1 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -16,24 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_tune_kspace.h" -#include -#include -#include -#include + #include "comm.h" -#include "update.h" +#include "compute.h" +#include "error.h" #include "force.h" #include "info.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "pair.h" -#include "error.h" -#include "memory.h" #include "timer.h" -#include "neighbor.h" -#include "modify.h" -#include "compute.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include +#include #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a)) diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h index 339f79626f93bfb47d0bae4e828b3b0ca83d323d..3e4db40344b30117996922b22bfbcca1e8ec570c 100644 --- a/src/KSPACE/fix_tune_kspace.h +++ b/src/KSPACE/fix_tune_kspace.h @@ -21,7 +21,7 @@ FixStyle(tune/kspace,FixTuneKspace) #define LMP_FIX_TUNE_KSPACE_H #include "fix.h" -#include + namespace LAMMPS_NS { diff --git a/src/KSPACE/gridcomm.cpp b/src/KSPACE/gridcomm.cpp index 4024670b9ff0571bf3a82297991bcdbe24cc6542..0f899d31cf693acbf16203b3f4ccc761fb53c969 100644 --- a/src/KSPACE/gridcomm.cpp +++ b/src/KSPACE/gridcomm.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "gridcomm.h" -#include + #include "comm.h" -#include "kspace.h" +#include "error.h" #include "irregular.h" +#include "kspace.h" #include "memory.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index 00bdac53db99a45b746c92a4d1fd32c0394b993d..d0f4d38686a07ea65c3688ffe1d624e92709ce98 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "msm.h" -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "gridcomm.h" +#include "math_const.h" +#include "memory.h" #include "neighbor.h" -#include "force.h" #include "pair.h" -#include "domain.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index 4742e4c48c2b0b80124170528f6d4357468b513c..a05a6a282b97cbfd9e06899918312b051da888d0 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index f589dfaa90aa24e1256f93bfd54b31203577f59b..8d15a6480aac75e820594203db74c5f8e5bf68c5 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_long.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index 3552e8bb86588cb19e8846f18a3dfe2d94730ccf..a845ddd1d2c75c2cdc3baaacf8d862f31ecafe82 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_long_coul_long.h" -#include + #include #include #include "math_vector.h" @@ -31,7 +31,7 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 60187ce90104f7cc2777442f75ce6ffec0fa3000..2520da2654288a2d98eccb5faaffbf13591b9d72 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index ff52720a08f3ac8cf296349ed6c42e37b0372d72..261e93fbc9288ca8063218f0b2b1c170d83cee15 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -29,7 +29,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index b10cdf2b08e93fe056aff228d67867b2a82bb4f7..9df9862c117a8c20f32399cd98ec98ba9e08369c 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index ef25055a76a9c8a8d82b21bc077223c3f987e909..7fd8a72559ce20bd86f6d7671793c21856696997 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index 426ec00e55c9b92f0b368e1f0030d898affbcddf..a62c1bd55b2f9a95e6a21fe950370dcf7a55a093 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 7b7a065e2220347fbf6ad29cb7d371882926a376..b6727c2c992931fb92416aabce23fcf8e31af8dd 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_coul_long.h" -#include + #include #include #include "math_vector.h" @@ -33,8 +33,8 @@ #include "respa.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index c71fee8206700614705114200d7e58f070b4980e..8f17bda0086574fda1836b674078a71ba1971149 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_long_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index ee7d4fed1b5c91db70e566ad3b4c6bcb5277ad39..54973c69c2b4845efc6a5e174d1aa27f0145f292 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long.h" -#include + #include #include #include "angle.h" @@ -30,7 +30,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 9ce8ded7ddf20859c1ed2722e9ba217c84d5a3f1..41ffec4f3b0c967381d06f6d494ac090e72dd3cc 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -19,28 +19,25 @@ ------------------------------------------------------------------------- */ #include "pppm.h" -#include -#include -#include -#include + +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" #include "gridcomm.h" +#include "math_const.h" +#include "math_special.h" +#include "memory.h" #include "neighbor.h" -#include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" -#include "domain.h" -#include "fft3d_wrap.h" #include "remap_wrap.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" -#include "math_special.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index fa5235d6eb99edf02c1f7b7e367663bea5fb4c28..b319014c7814fd35392a177668c38dfa33266680 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -16,20 +16,18 @@ ------------------------------------------------------------------------- */ #include "pppm_cg.h" -#include -#include -#include + #include "atom.h" -#include "gridcomm.h" #include "domain.h" #include "error.h" -#include "force.h" -#include "neighbor.h" -#include "memory.h" +#include "gridcomm.h" #include "math_const.h" +#include "memory.h" +#include "neighbor.h" #include "remap.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole.cpp b/src/KSPACE/pppm_dipole.cpp index 1a87c81beebae4d981a29831c73406bb6f2be8a7..1b7d3253268ff2f79a02695c8799c7e718214a08 100644 --- a/src/KSPACE/pppm_dipole.cpp +++ b/src/KSPACE/pppm_dipole.cpp @@ -16,26 +16,23 @@ ------------------------------------------------------------------------- */ #include "pppm_dipole.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "force.h" -#include "pair.h" #include "domain.h" +#include "error.h" #include "fft3d_wrap.h" -#include "remap_wrap.h" +#include "force.h" +#include "gridcomm.h" +#include "math_const.h" +#include "math_special.h" #include "memory.h" -#include "error.h" +#include "pair.h" +#include "remap_wrap.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" -#include "math_special.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_dipole_spin.cpp b/src/KSPACE/pppm_dipole_spin.cpp index 4e33c117938733ae2ae968b10f7f5d74311e5d48..595c257331a4e7b784f6497884efa53874ae880d 100644 --- a/src/KSPACE/pppm_dipole_spin.cpp +++ b/src/KSPACE/pppm_dipole_spin.cpp @@ -16,22 +16,19 @@ ------------------------------------------------------------------------- */ #include "pppm_dipole_spin.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "gridcomm.h" -#include "force.h" -#include "pair.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "gridcomm.h" +#include "math_const.h" +#include "memory.h" +#include "pair.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" -#include "math_const.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index fba3f279383a114357d69a2589711756b3bf4626..a484751a8164c521bf3e62b8da8cd56b3f448cea 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -17,26 +17,24 @@ ------------------------------------------------------------------------- */ #include "pppm_disp.h" -#include -#include -#include -#include -#include "math_const.h" + +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fft3d_wrap.h" +#include "force.h" #include "gridcomm.h" +#include "math_const.h" +#include "memory.h" #include "neighbor.h" -#include "force.h" #include "pair.h" -#include "bond.h" -#include "angle.h" -#include "domain.h" -#include "fft3d_wrap.h" #include "remap_wrap.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/KSPACE/remap_wrap.cpp b/src/KSPACE/remap_wrap.cpp index 7929cd053c7dd81943739b8ffdb1e497a2636c7d..4aaaa1329ed8396c55fbce4ccbf2b0b8c60368ee 100644 --- a/src/KSPACE/remap_wrap.cpp +++ b/src/KSPACE/remap_wrap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "remap_wrap.h" -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index b8bbba73dabe5abf45ea027ceb55f4613fa548a8..54169d08d71c92677429e07a9848d3bdf15693c4 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_comb.h" -#include + #include #include #include "pair_comb.h" @@ -30,8 +30,8 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 74fd03e080d4731f2ef1f91163f01208065f7edf..ff30ac7b1e9822f664ed104a6894979304af847a 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_adp.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 6d783545f7e4d3827535cb7480f3c3c380da8b27..7ab2eaa27b1ef5d948f953e41cdca068fcdf4054 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -21,23 +21,23 @@ ------------------------------------------------------------------------- */ #include "pair_airebo.h" -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "my_page.h" +#include "error.h" +#include "force.h" #include "math_special.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" -#include "fmt/format.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index 60905fd2ffd9fc85b7ad01abb150518176cc7b8b..2a69e70b811f9a4870d0bf1e715c7db4308bf585 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_atm.h" -#include + #include #include "atom.h" #include "citeme.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index 5b080c9f0e6311f5c1f0fa0be294e5fef53bd6ca..e7c2f64672b11174c0e63a44c9235352ce7b3a25 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -33,22 +33,21 @@ ------------------------------------------------------------------------- */ #include "pair_bop.h" -#include -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" -#include "fmt/format.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp index 6b8d4e428e0be0b8b23e5a9cd4fccd14dabd7358..a27aaef4ab95991523127d646a4f1d756b0bde94 100644 --- a/src/MANYBODY/pair_comb.cpp +++ b/src/MANYBODY/pair_comb.cpp @@ -19,9 +19,9 @@ ------------------------------------------------------------------------- */ #include "pair_comb.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -34,7 +34,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp index 385e3ca35db17946fbae877f9db51fdc31c56eef..265d30c6f71df82389a57f01e03ca45df5eb0154 100644 --- a/src/MANYBODY/pair_comb3.cpp +++ b/src/MANYBODY/pair_comb3.cpp @@ -18,25 +18,24 @@ ------------------------------------------------------------------------- */ #include "pair_comb3.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "my_page.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "group.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "my_page.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" -#include "fmt/format.h" +#include "text_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index 159ba55a29e597e02c573d11e7c6dd45458613fb..999384ea2f5d6d4c7391164f742b474f04ec63aa 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_eam.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp index 3e33d40ee47cab9ea8c9b4542177594fb2d317cd..d30f46aa3620bf3227aa61608469cabe984253aa 100644 --- a/src/MANYBODY/pair_eam_alloy.cpp +++ b/src/MANYBODY/pair_eam_alloy.cpp @@ -16,16 +16,15 @@ ------------------------------------------------------------------------- */ #include "pair_eam_alloy.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 4f5041090f1c73a9aa2b2570017bd0eb86698da1..dc36c73272e8144bc6eac5036e71820adc056666 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_eam_cd.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -29,8 +29,8 @@ #include "memory.h" #include "error.h" #include "tokenizer.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp index fbe6bee529ef0e179cceaf2cf441f650539bd481..dd45d12da336924286f1a873b3f886cf56343c8f 100644 --- a/src/MANYBODY/pair_eam_fs.cpp +++ b/src/MANYBODY/pair_eam_fs.cpp @@ -16,16 +16,15 @@ ------------------------------------------------------------------------- */ #include "pair_eam_fs.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index cdd928788b69858f12768dedf69d90df96008700..cb5a95faa2731c8b64e9e787c2e666c8e41e30db 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -16,20 +16,18 @@ ------------------------------------------------------------------------- */ #include "pair_eim.h" -#include -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include "tokenizer.h" -#include "potential_file_reader.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h index 1266ffd242e7ef748cde9e3ec4b81fdeeb8af639..75f8ea6beaa25be2b083d4dcf97bc251f567bebd 100644 --- a/src/MANYBODY/pair_eim.h +++ b/src/MANYBODY/pair_eim.h @@ -21,7 +21,7 @@ PairStyle(eim,PairEIM) #define LMP_PAIR_EIM_H #include "pair.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index 0928d1469657e899eec9839a2dc24eecd497ad77..051c30f8733868da3fb434f9f9f06982d32c5445 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_gw.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp index 1a2bf5eb5d1bbb396195b2752c2ee07717d600e1..ee3bebda133169cea8fd4520e5360aa9888e27e2 100644 --- a/src/MANYBODY/pair_gw_zbl.cpp +++ b/src/MANYBODY/pair_gw_zbl.cpp @@ -17,21 +17,18 @@ ------------------------------------------------------------------------- */ #include "pair_gw_zbl.h" -#include -#include -#include -#include -#include "atom.h" -#include "update.h" -#include "force.h" + #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "math_const.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include -#include "math_const.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 56ef70d8f966e0f9a8a1fd2ab0e0e9c0008de324..d2e478b37dd52ea4ee71659ceb12ee2b5d9015dd 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lcbop.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index dc537a7b587b30f5b83a5f43f73c69d70b0a2b6e..0a197a157603825faf2a3314d3dc2cac631568d1 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_nb3b_harmonic.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 502580719a020866974f29fe7acb263df0f96394..0f7fd7a1c7bc4dee87e98590995f71537e8f5c1d 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -17,21 +17,20 @@ ------------------------------------------------------------------------- */ #include "pair_polymorphic.h" -#include -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h index 18956699d71793b1312d94df717185dfe72d63c5..2593905b227db369882513dc60b4e9623945523e 100644 --- a/src/MANYBODY/pair_polymorphic.h +++ b/src/MANYBODY/pair_polymorphic.h @@ -22,7 +22,6 @@ PairStyle(polymorphic,PairPolymorphic) #include "pair.h" #include -#include namespace LAMMPS_NS { diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index f6b5a803d25dbfa99542190881e929f878824198..2deb45ac75a5da5ef3fca043a8c7f9250c10dc0e 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -16,21 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_sw.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "utils.h" -#include "tokenizer.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index c57740963f0a9a9f95fe0cda8b7ae7494d54a953..c08c722e5f9e80b59ba0475db5db62b845f31f3e 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -16,24 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff.h" -#include -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" -#include "potential_file_reader.h" - +#include "force.h" #include "math_const.h" #include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp index d1ab6f203483993c44b94735895f0688aff9483c..ea40125ce4868c6984855ffe466167578da1973d 100644 --- a/src/MANYBODY/pair_tersoff_mod.cpp +++ b/src/MANYBODY/pair_tersoff_mod.cpp @@ -17,20 +17,17 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod.h" -#include -#include -#include -#include -#include "atom.h" -#include "force.h" + #include "comm.h" +#include "error.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "tokenizer.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp index ff8916cdcde18ecf7d76604d73c532276855fb5d..6a6497afae5dae53ecbb277f2ec5c9850d93c083 100644 --- a/src/MANYBODY/pair_tersoff_mod_c.cpp +++ b/src/MANYBODY/pair_tersoff_mod_c.cpp @@ -16,18 +16,15 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_mod_c.h" -#include -#include -#include -#include -#include "atom.h" -#include "force.h" + #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp index 141cb45964a0ca03aea237ecfcf64c46cce6fcfe..fad89195b2f6c53ef882710fe1813e7f586362d0 100644 --- a/src/MANYBODY/pair_tersoff_zbl.cpp +++ b/src/MANYBODY/pair_tersoff_zbl.cpp @@ -17,21 +17,18 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_zbl.h" -#include -#include -#include -#include -#include "atom.h" -#include "update.h" -#include "force.h" + #include "comm.h" -#include "memory.h" #include "error.h" #include "math_const.h" #include "math_special.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index 815854a34b61aa9d0256279df55b44de53d81231..63765234b3948f86c506f0ffeec1fa0007ff1dff 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "pair_vashishta.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp index 53338f08dcdeb25ee7ab952e11153423e40e875f..f786179aa4ceaaab0ed95ec2e654ae3b4a87aeb7 100644 --- a/src/MC/fix_atom_swap.cpp +++ b/src/MC/fix_atom_swap.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_atom_swap.h" -#include + #include #include #include diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp index 833a071694b95a7da1146aed97e3c037aaa557b1..8a7cd20b0f9c0fa26c73027d73ea06b26de919a4 100644 --- a/src/MC/fix_bond_break.cpp +++ b/src/MC/fix_bond_break.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_break.h" -#include + #include #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp index 9603fc1583adbc5daeba85c0163c1cfbfb25017d..a2c2eee2c5cb19e9df9ea13db8f651bf8d094e79 100644 --- a/src/MC/fix_bond_create.cpp +++ b/src/MC/fix_bond_create.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_create.h" -#include + #include #include "update.h" #include "respa.h" diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp index 82b27d490fc55db39b7f43e8dd72ecb247d07dd8..270a497772c1a3ae03101361cba441d477b931f8 100644 --- a/src/MC/fix_bond_swap.cpp +++ b/src/MC/fix_bond_swap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_bond_swap.h" -#include + #include #include #include "atom.h" diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index f286ab6807ea1a35793e1707cf0ba619ae2f155b..fc306696eda0a22a769985927cbfec2cb6f2ff14 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_gcmc.h" -#include + #include #include #include "atom.h" diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp index cf327dc2e1b3526cf64e496457b755aa09cb0797..b855c0b79e35e9da035ec7266d5d6d081f3c1164 100644 --- a/src/MC/fix_tfmc.cpp +++ b/src/MC/fix_tfmc.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_tfmc.h" -#include + #include #include #include diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index 7f6f7ae1bde1c06dc152afd050fb8829e01c6ca1..94b248174272002cfd9ed5b654459702150a8e26 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -15,38 +15,35 @@ Contributing author: Evangelos Voyiatzis (Royal DSM) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_widom.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "atom_vec_hybrid.h" -#include "molecule.h" -#include "update.h" -#include "modify.h" -#include "fix.h" +#include "bond.h" #include "comm.h" #include "compute.h" -#include "group.h" +#include "dihedral.h" #include "domain.h" -#include "region.h" -#include "random_park.h" +#include "error.h" +#include "fix.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "thermo.h" -#include "output.h" +#include "modify.h" +#include "molecule.h" #include "neighbor.h" -#include +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace std; using namespace LAMMPS_NS; diff --git a/src/MC/fix_widom.h b/src/MC/fix_widom.h index 05060e76ac71bf5d90f7faa9a9c354688fcaf1c3..19102e4f4ac0ab53e89572ebfe399abfe62c8d4e 100644 --- a/src/MC/fix_widom.h +++ b/src/MC/fix_widom.h @@ -20,7 +20,6 @@ FixStyle(widom,FixWidom) #ifndef LMP_FIX_WIDOM_H #define LMP_FIX_WIDOM_H -#include #include "fix.h" namespace LAMMPS_NS { diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp index 30c66a671fb958ede354519c7b2dc081991846b8..588d57f324ad01fa1dbf4de088488f6e779b8091 100644 --- a/src/MC/pair_dsmc.cpp +++ b/src/MC/pair_dsmc.cpp @@ -16,19 +16,17 @@ ------------------------------------------------------------------------- */ #include "pair_dsmc.h" -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "domain.h" -#include "update.h" #include "random_mars.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp index 6123bf49afec6f851fa9301769b537622063060d..7f4e6b1f3c7170b3c51e1a4b642e096375d0ecc8 100644 --- a/src/MISC/compute_msd_nongauss.cpp +++ b/src/MISC/compute_msd_nongauss.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_msd_nongauss.h" -#include + #include "atom.h" #include "update.h" #include "group.h" diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp index 286770017c3b1627b65f7a58bc26ecffbf8b0854..d8be8679c6956fd2c6e3f8575bddd82b6f1dfad2 100644 --- a/src/MISC/compute_ti.cpp +++ b/src/MISC/compute_ti.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_ti.h" -#include + #include #include "atom.h" #include "update.h" @@ -27,7 +27,7 @@ #include "input.h" #include "variable.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp index fbd56b909601585c08326e5b7d8e60822dc7140d..9f2bbfe424f7ce4f68e84617e5c98797710ad6d8 100644 --- a/src/MISC/dump_xtc.cpp +++ b/src/MISC/dump_xtc.cpp @@ -24,7 +24,7 @@ #include "dump_xtc.h" #include -#include + #include #include #include "domain.h" diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp index 7d9766c57c3049b6dbb79f6d38a6a8ee5d5a848f..7ee6fce1b979ac6588c9430255b7000f5481f781 100644 --- a/src/MISC/fix_deposit.cpp +++ b/src/MISC/fix_deposit.cpp @@ -12,26 +12,25 @@ ------------------------------------------------------------------------- */ #include "fix_deposit.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "fix.h" #include "lattice.h" -#include "region.h" -#include "random_park.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "molecule.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp index 0dc0be494722253b4c29ab76c1ee2d3031f9d1ee..bd2f9acfb91879076c46c80766593dc419056914 100644 --- a/src/MISC/fix_efield.cpp +++ b/src/MISC/fix_efield.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_efield.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp index 153de8851b551cac08f0802d38270597fba61d66..6396d139a0a1aa982c775d02678c4e37131e5a6d 100644 --- a/src/MISC/fix_evaporate.cpp +++ b/src/MISC/fix_evaporate.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_evaporate.h" -#include + #include #include "atom.h" #include "atom_vec.h" diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp index c4ff1ebeba4296414b74aef8ea841a4ec5d33ddf..75642b632f8b8e8cad04dad9802c584a4d045767 100644 --- a/src/MISC/fix_gld.cpp +++ b/src/MISC/fix_gld.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_gld.h" -#include + #include #include #include "atom.h" diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp index d2bef7cb9bd216dab3b8931390a7cbbd0255a42c..1ca24a5906bbc15da52d356f43f158887ef7309c 100644 --- a/src/MISC/fix_oneway.cpp +++ b/src/MISC/fix_oneway.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_oneway.h" -#include + #include "atom.h" #include "domain.h" #include "error.h" -#include "force.h" #include "region.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp index 3141f6496ccac41c09881b1319bfa0560d17a010..cc22a509ba9aebd82bf1a06857ec2fcc98fc0cfb 100644 --- a/src/MISC/fix_orient_bcc.cpp +++ b/src/MISC/fix_orient_bcc.cpp @@ -19,25 +19,21 @@ ------------------------------------------------------------------------- */ #include "fix_orient_bcc.h" -#include -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "citeme.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "math_const.h" -#include "citeme.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp index bcba14c355b16df378d00b8f2a689260fee83fe3..f391eab91e3280291da9c602a414c89ff098947f 100644 --- a/src/MISC/fix_orient_fcc.cpp +++ b/src/MISC/fix_orient_fcc.cpp @@ -16,25 +16,21 @@ ------------------------------------------------------------------------- */ #include "fix_orient_fcc.h" -#include -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "citeme.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "math_const.h" -#include "citeme.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp index 7eec60be8bb64057dcf580448ec1e4e644126c19..115045db81d4d36ceee158657666a69a8f0979a0 100644 --- a/src/MISC/fix_thermal_conductivity.cpp +++ b/src/MISC/fix_thermal_conductivity.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_thermal_conductivity.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 24f988a76daa173ebd82985809ab72a1fad68cdd..2d38f3c6c695caba3b5d16793ef519472896e838 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_ttm.h" -#include + #include #include #include "atom.h" @@ -29,8 +29,8 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp index b8c04132ea29c8af6deb0745abaa107b635ee7d1..5dcd2d291d7a5813f15233c7d11995a177cff8bc 100644 --- a/src/MISC/fix_viscosity.cpp +++ b/src/MISC/fix_viscosity.cpp @@ -17,14 +17,14 @@ ------------------------------------------------------------------------- */ #include "fix_viscosity.h" -#include -#include -#include + #include "atom.h" #include "domain.h" -#include "modify.h" #include "error.h" -#include "force.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index e2e6f408570d3549e23f70bf0181fccaf383f4e5..4fc1fb0628bb3faff8a2118d27c0dbcbb007dcc5 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index efc84f22b52e985d29cdbc762372227a5ffefcfa..4a18680415295c8c07ad00663b0e6cbf2c890e6f 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_cut.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 79b1ebae66d8e6eaac27dd5d0fd4020e3ef29533..576637c593ad22786b960194cdfe727eb0c82e5c 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_nm_cut_coul_long.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MLIAP/compute_mliap.cpp b/src/MLIAP/compute_mliap.cpp index 134994f829a067354e587123e4265b9ddb2896d8..956cb0196f1f0758a8495ee487d8f3e700cbf353 100644 --- a/src/MLIAP/compute_mliap.cpp +++ b/src/MLIAP/compute_mliap.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "mliap_data.h" #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" @@ -22,7 +22,6 @@ #include "update.h" #include "modify.h" #include "neighbor.h" -#include "neigh_list.h" #include "neigh_request.h" #include "force.h" #include "pair.h" diff --git a/src/MLIAP/compute_mliap.h b/src/MLIAP/compute_mliap.h index 5602ace89b81917c0e0bd2fc2106a712b31e09c5..1172111247619df60e975e917d653770824a51e3 100644 --- a/src/MLIAP/compute_mliap.h +++ b/src/MLIAP/compute_mliap.h @@ -21,7 +21,7 @@ ComputeStyle(mliap,ComputeMLIAP) #define LMP_COMPUTE_MLIAP_H #include "compute.h" -#include + namespace LAMMPS_NS { diff --git a/src/MLIAP/mliap_data.cpp b/src/MLIAP/mliap_data.cpp index 7bffd8ec3b19d6c0d289733d87a36ab0c0876099..a7e50012cb484e8529fe2e1c16a04d68e46355cf 100644 --- a/src/MLIAP/mliap_data.cpp +++ b/src/MLIAP/mliap_data.cpp @@ -11,24 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "mliap_data.h" -#include "mliap_model_linear.h" -#include "mliap_model_quadratic.h" -#include "mliap_descriptor_snap.h" -#include "compute_mliap.h" + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "pair.h" -#include "comm.h" #include "memory.h" -#include "error.h" +#include "mliap_descriptor.h" +#include "mliap_model.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_descriptor.cpp b/src/MLIAP/mliap_descriptor.cpp index d654b330081b1275135703714ea2430070c8f17e..63d4241e019cc3ffde1efd41f7e85e00d36d56ef 100644 --- a/src/MLIAP/mliap_descriptor.cpp +++ b/src/MLIAP/mliap_descriptor.cpp @@ -12,14 +12,9 @@ ------------------------------------------------------------------------- */ #include "mliap_descriptor.h" -#include "atom.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; -#define MAXLINE 1024 -#define MAXWORD 3 /* ---------------------------------------------------------------------- */ diff --git a/src/MLIAP/mliap_descriptor_snap.cpp b/src/MLIAP/mliap_descriptor_snap.cpp index fd1bf18330ce669d70cce1abbff5bdc1d5ffdddc..5f0ee33c8c4e23d48d035fcfc0b1a61e7100c0e2 100644 --- a/src/MLIAP/mliap_descriptor_snap.cpp +++ b/src/MLIAP/mliap_descriptor_snap.cpp @@ -12,20 +12,17 @@ ------------------------------------------------------------------------- */ #include "mliap_descriptor_snap.h" -#include "pair_mliap.h" -#include "mliap_data.h" -#include -#include -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "utils.h" -#include "sna.h" -#include "memory.h" #include "error.h" -#include "fmt/format.h" +#include "memory.h" +#include "mliap_data.h" +#include "pair_mliap.h" +#include "sna.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_model.cpp b/src/MLIAP/mliap_model.cpp index b8ad1913a0014750164d6550d88daed63e5a8951..b731e1c9f809e27c8644484d817582c6681898a7 100644 --- a/src/MLIAP/mliap_model.cpp +++ b/src/MLIAP/mliap_model.cpp @@ -12,17 +12,12 @@ ------------------------------------------------------------------------- */ #include "mliap_model.h" -#include "pair_mliap.h" -#include -#include -#include "atom.h" -#include "force.h" + #include "comm.h" -#include "utils.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "fmt/format.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/MLIAP/mliap_model_linear.h b/src/MLIAP/mliap_model_linear.h index 67ba0985a2b4df3602b26d76a62d624602bbc387..326407faa84deb50b4b3bea190853a2879e4fd25 100644 --- a/src/MLIAP/mliap_model_linear.h +++ b/src/MLIAP/mliap_model_linear.h @@ -20,7 +20,7 @@ namespace LAMMPS_NS { class MLIAPModelLinear : public MLIAPModel { public: - MLIAPModelLinear(LAMMPS*, char* = NULL); + MLIAPModelLinear(LAMMPS*, char* = nullptr); ~MLIAPModelLinear(); virtual int get_nparams(); virtual int get_gamma_nnz(class MLIAPData*); diff --git a/src/MLIAP/pair_mliap.cpp b/src/MLIAP/pair_mliap.cpp index f2e042141c78d06941cf3ec4372d546fc9e115c9..4c6d90678786dab883de92e142623e85de08a4f2 100644 --- a/src/MLIAP/pair_mliap.cpp +++ b/src/MLIAP/pair_mliap.cpp @@ -11,22 +11,22 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include -#include -#include +#include "pair_mliap.h" + #include "mliap_data.h" #include "mliap_model_linear.h" #include "mliap_model_quadratic.h" #include "mliap_descriptor_snap.h" -#include "pair_mliap.h" + #include "atom.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "memory.h" -#include "error.h" +#include "neigh_request.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 117056ac58ff00cdd332b6ff40406e5d0c696065..6cd550384d61c6e2a64d7310afdc1146dfcd53da 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_charmm.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 732843f412d98f10748c43fe033af305f76d1198..0288a61d8330c3332d708267d2fc9d3165034b93 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index 2ec59bfb1ee9c913b37fcc79d044f7e103c242f6..1a05edc20bf7a6992db08b23b30238dcc7f919ac 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_periodic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index ac276511a25290ea82d23531b1b76ab2ce9a92b5..5fb40b54c9dff1890e5e8d5c7967bd870e5e8365 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_squared.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 02bab37a8a979fd3e4ecbd8227d91ed6ef2a8f5f..eb5e48ec9b87c7b9d617596833d0b6cc861724ed 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "angle_harmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 83e4485d481f099a6aed54e230f62602073b1d7f..100b75cb0a1d7399fa99929cb959c717e7f1b9c3 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "angle_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,10 +28,10 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp index 97d4c865baca9947ae8332a3491e1d8b4a99d742..ead8de7cb575523c1092f18bad17972ee5b1fe15 100644 --- a/src/MOLECULE/atom_vec_template.cpp +++ b/src/MOLECULE/atom_vec_template.cpp @@ -12,15 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_template.h" + #include "atom.h" -#include "molecule.h" -#include "comm.h" -#include "domain.h" -#include "modify.h" -#include "fix.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "molecule.h" using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 9617894a9a66ba7ce68bada3e303d0d4ffcea5be..b2271d45fcf0fd78df8580288358473cc8653f11 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_fene.h" -#include + #include #include #include "atom.h" @@ -22,8 +22,8 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index eec8c14872d5e0c008ccb6d547fb8382a212e247..676d5f6871eeb31a144892156aff6a396ad6ac5a 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_fene_expand.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 4e20a2711d65032e57f513d6da17dd83129f141f..89b3830cb53adc2678e876347827354ad5534687 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_gromos.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index 773a4ee12a91df47ae8f115def961074e121bb9d..28100512a8c398c6cfea283c480f96df0fc9652a 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 38d8d6a45f1e6882be425698cf114510ba56348a..49074e1cdc393430f16f3da262c0cba29aa68c1a 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_morse.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 1733ffc6706312fe46656024ef7069423a2d585b..63b640730af0651775c862af628ff5ee6044b8cd 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "bond_nonlinear.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index c89ac552aead1ed9b38926fb19dd2adeadf9dfad..c8d182e4ffaf97fe0a5b067e78018ef3de31fd6e 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_quartic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "pair.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 2724d4f20c349a66ae0365c6671cade2957494ae..5cc91ceae09c2a88f8ced4a97648ed66d0f176e0 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "bond_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,10 +26,10 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 71c9f586a3161d13b2569ecc512b0d5e39afcd1c..11422e0820df1101d0af4bf09629c971f40aae8f 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmm.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index d4956b42bd290e94b1f9107c7f6b3c428aa93962..408be8ef9986cc633234dffd8610480e02308248 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_charmmfsw.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index 403bafd23e228c6c40aebdf4189e8d6f5e33e30e..55e2f250061dcf680e82d4f322dbdfb39b5dd220 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index ce31a12ed3f030eb464f00e9a5ec4941c983a0b7..40e026c2f1f45059ecc310d1b2c6708e89335897 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_helix.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index a3c76b91ee74ec493a51766d49b3dbe09bcb5519..963304da80ad884054929f00c252f2f4f16a60c4 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_multi_harmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index 151986ca3f68b1de8171ff540f4bcf194140e563..fe05dc7c3d0a1cf3fb9df28eda21b1679f85a5f4 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_opls.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index ddf035070b679d9a899d2ecf1d8e673f949d1565..2de6dd418313eeb96b08db6f775cff7639682b06 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -28,9 +28,9 @@ ------------------------------------------------------------------------- */ #include "fix_cmap.h" -#include + #include -#include + #include #include "atom.h" #include "update.h" @@ -41,8 +41,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index d819642bb10b42c0217173c457afe98303f421f7..90cf3eee3915584392491d4b569504971ca5355d 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_cvff.h" -#include + #include #include "atom.h" #include "comm.h" @@ -21,7 +21,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 2af1126876a6a3c7e76090db5e4589e2b593cbb8..6327ea8b06476ff2c81d692fdf4eac0a58f51a7a 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 1f2da63486fa549621c1204f870b9cdc0f73dc7b..7b2c4e0b09520238542d7bbf429f0a905565e2c3 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_umbrella.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index 69ea81a0176b7705947649433c8ae8592fb1b29b..6d9c851422b0729cf24d3725e373d16fd3f2767f 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -30,7 +30,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index 8d6dfc7d68d8c88366d4d8ce216abe06234d3326..422da8d827e003a5be7a1a8669ebdd410e6620bf 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -30,7 +30,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index f09f9a483acea6f6a4b37fb185af74f61dc49c7b..dea6bd62514e014aa211f85cf25b817831b9f702 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_charmm.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index e646392e0e29a4238798de98cbe93fd6ad93ee3b..31083312a9c2f72f3f59dd2008bf3a232d7e8665 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmmfsw_coul_charmmfsh.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index b23195086c192b135649fcf6d30ab5e1a6244fd8..b5ed2557890980b38de4ded4378af87822cea327 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index bea8acbcbcd6c50aa7b7d52e743f057060497241..8d8f5ec78ec5810ce7607aee5ac843bd321fa149 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_cut.h" -#include + #include #include "atom.h" #include "force.h" @@ -28,7 +28,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp index 9d15e8b1a88c44cfb18cd36dac31c03dada15528..62d940af3717dc6e91aed907d346e61dce7145bf 100644 --- a/src/MPIIO/dump_atom_mpiio.cpp +++ b/src/MPIIO/dump_atom_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_atom_mpiio.h" #include -#include + #include #include "domain.h" #include "update.h" diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp index bca19e58c87230e5f2774ce17fce2e41af63f93d..6d5fc3da8e6f756a5446c2bcd2d713840c65e035 100644 --- a/src/MPIIO/dump_cfg_mpiio.cpp +++ b/src/MPIIO/dump_cfg_mpiio.cpp @@ -17,15 +17,16 @@ #include "omp_compat.h" #include "dump_cfg_mpiio.h" -#include -#include -#include + #include "atom.h" #include "domain.h" #include "update.h" #include "memory.h" #include "error.h" +#include +#include + #ifdef LMP_USER_IO_TIMER #include #include diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp index 3f9c09738e9bc09ec5768bdc902c47212e1bf922..b623df82d086598f35ae2e18a298fce730f6ffdd 100644 --- a/src/MPIIO/dump_custom_mpiio.cpp +++ b/src/MPIIO/dump_custom_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_custom_mpiio.h" #include -#include + #include #include "domain.h" #include "input.h" diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp index d1b2d5079ab57edcfec7760a77335092b7de9461..139245e4b0ad8da087d88ed29523b3f1445710e6 100644 --- a/src/MPIIO/dump_xyz_mpiio.cpp +++ b/src/MPIIO/dump_xyz_mpiio.cpp @@ -18,7 +18,7 @@ #include "omp_compat.h" #include "dump_xyz_mpiio.h" #include -#include + #include #include "domain.h" #include "update.h" diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp index 66c7d8a4170c25621081e34c872441b2676dca8d..b2caa411e3572c0873339079fae7ff6e65762d04 100644 --- a/src/MPIIO/restart_mpiio.cpp +++ b/src/MPIIO/restart_mpiio.cpp @@ -16,8 +16,7 @@ ------------------------------------------------------------------------- */ #include "restart_mpiio.h" -#include -#include + #include "error.h" using namespace LAMMPS_NS; diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp index 9c9e415be5136dead7c279ca1a9199ddfbb98e07..29d6d550e415788e17a0cca646f72165517ba4d7 100644 --- a/src/MSCG/fix_mscg.cpp +++ b/src/MSCG/fix_mscg.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_mscg.h" -#include + #include -#include + #include "mscg.h" #include "atom.h" #include "comm.h" diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index e6b6fb72f4247562386bfc07fa6bf6b037263c55..82510e817798387cc6f5e2b558ac25e6e91d5d10 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -21,7 +21,7 @@ #include "pair_eam_opt.h" #include -#include + #include "atom.h" #include "comm.h" #include "force.h" diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index 3dc6bdb6b4ea769309457f2d410e448be1f7af86..a7fbfb823a2979a2525d738390755a5194615a25 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -20,7 +20,7 @@ #include "pair_lj_charmm_coul_long_opt.h" #include -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index 3b3a19a9e8eff985f555fef08ffc908d77c1822c..a31f521ecc68180f8f51716f8ad347aab580d27d 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_opt.h" -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index 1d2e226777eb3b549d85602f7952690a48e0892f..89d254ee0439d20af10e6b409b469c28341d4749 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -20,7 +20,7 @@ #include "pair_morse_opt.h" #include -#include + #include "atom.h" #include "force.h" #include "neigh_list.h" diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index d824d82e6c37f6769ac117a8672fa1606937020d..2cb5323745f51f146de72cc7901603102ac7a31f 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_ufm_opt.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp index 5ce74575ba479c6821caa96d1a4f2710c802ec2a..ada25431c8af4f6c6c3d1eb6af88025e5481533a 100644 --- a/src/PERI/atom_vec_peri.cpp +++ b/src/PERI/atom_vec_peri.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "atom_vec_peri.h" -#include -#include + #include "atom.h" #include "citeme.h" -#include "memory.h" #include "error.h" +#include +#include + using namespace LAMMPS_NS; static const char cite_peri_package[] = diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp index 022eb0bab6cd9c54c5239c3d68cd587584d23d03..295038119735d2e65fd8fdcbce3c69a7d04ee857 100644 --- a/src/PERI/fix_peri_neigh.cpp +++ b/src/PERI/fix_peri_neigh.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_peri_neigh.h" -#include + #include #include "pair_peri_lps.h" #include "pair_peri_ves.h" diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 5e3a514b617ff4e9c4108fe115e9c0744b40835f..0e5760ac8df7eb87c4e644f20692b5e6dd448ddd 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -16,24 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_peri_eps.h" -#include -#include -#include -#include + #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "math_const.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index e73e2eff677d2ff89bb46543582d1bd6379fda9c..b60f28d9f12556b2c2ba830f873de2b5ea16ea89 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -16,24 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_peri_lps.h" -#include -#include -#include -#include + #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "math_const.h" +#include "neighbor.h" + +#include using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index cf751885d6fc7569cdeaaaec1985590c2b6f1f3b..5d6973a9151b670ed4bf315c94a16c59c5bd747a 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -16,24 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_peri_pmb.h" -#include -#include -#include -#include -#include + #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 138584123af1f3efa32dbb4641cd624c31fc5cc6..93c980702bd8350eff7fbe3ddb8ead0b12aa21d0 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -16,25 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_peri_ves.h" -#include -#include -#include -#include + #include "atom.h" +#include "comm.h" #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix_peri_neigh.h" #include "force.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "fix_peri_neigh.h" -#include "comm.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index b0b1287717e102efad59a32cc1c1a28a1795a269..12dc59c28681316742f3c2047bd17a042a95972e 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -18,10 +18,10 @@ ------------------------------------------------------------------------- */ #include "fix_poems.h" -#include + #include #include -#include + #include "workspace.h" #include "atom.h" #include "domain.h" @@ -34,8 +34,8 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 767c22c49634958769328ec70f68d505da3f1931..8966d9a9db621ebf640e036081147e3e55b84295 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_python_invoke.h" -#include // IWYU pragma: keep -#include -#include "force.h" -#include "update.h" + #include "error.h" #include "lmppython.h" #include "python_compat.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index be63b851a2b62062d64689c611b21d75cdbb85a2..53bde5e8045a1e0957c0a264b18b80782fbd0410 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -16,12 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_python_move.h" -#include // IWYU pragma: keep -#include -#include "lmppython.h" + #include "error.h" +#include "lmppython.h" #include "python_compat.h" +#include +#include // IWYU pragma: export + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index d0650bcb51a16063b1eed9af507d2bf4e3503e47..074de2f39a64c3eadfdabe811851392581658dad 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -16,17 +16,18 @@ ------------------------------------------------------------------------- */ #include "pair_python.h" -#include // IWYU pragma: keep -#include -#include + #include "atom.h" +#include "error.h" #include "force.h" +#include "lmppython.h" #include "memory.h" -#include "update.h" #include "neigh_list.h" -#include "lmppython.h" -#include "error.h" #include "python_compat.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; diff --git a/src/PYTHON/python_compat.h b/src/PYTHON/python_compat.h index 175d797ffa150589fe8d0bedb901c3a6527c3867..effac81cef8304c13f6e3dc63c10685933e1e4f6 100644 --- a/src/PYTHON/python_compat.h +++ b/src/PYTHON/python_compat.h @@ -14,6 +14,8 @@ #ifndef LMP_PYTHON_COMPAT_H #define LMP_PYTHON_COMPAT_H +#include + // Wrap API changes between Python 2 and 3 using macros #if PY_MAJOR_VERSION == 2 #define PY_INT_FROM_LONG(X) PyInt_FromLong(X) diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index b54abe28b0d144ec972ec2e01af494c6b8b9886d..cb35cba85ae6800495162244782394af8e4b4f82 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Richard Berger and Axel Kohlmeyer (Temple U) + Contributing authors: Richard Berger and Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ #include "python_impl.h" -#include -#include -#include // IWYU pragma: keep -#include "force.h" + +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" #include "python_compat.h" +#include "variable.h" + +#include +#include // IWYU pragma: export using namespace LAMMPS_NS; diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index ba4932a485a7adb74d5745afc920cb5997248c6f..5cadce617f40a4296fb1521b0619d20d6eacadd6 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index a2cc683b564df03727a1f0a7f3b3c74162f3628e..7f50736b188f1c32ac6e215bbf2d75786effa5e4 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_dynamic.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 265528a089ca0ae72fe779c55ae2699bc4dbf14b..6dcc5e9cdca813e35bf82c8a3e521ad7028841e5 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_fire.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 4f5369eb877890cf4a36d9a72710f65fc276a481..327a9c5b3ae7f89739763c26158c83524f001d83 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -17,7 +17,7 @@ #include "fix_qeq_slater.h" #include -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp index e130f85f5ffffc2c68fdf198898b37b2a9e341b3..531f488e60426debfefc964d8cea917291175ca2 100644 --- a/src/REPLICA/compute_event_displace.cpp +++ b/src/REPLICA/compute_event_displace.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "compute_event_displace.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "modify.h" -#include "fix_event.h" #include "error.h" -#include "force.h" +#include "fix_event.h" +#include "modify.h" #include "update.h" +#include + using namespace LAMMPS_NS; #define INVOKED_SCALAR 1 diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp index ddbe10adc94baca2a4063c17ea3d9f15aa32db88..ba784cc3e98c88368798f5c4ce909f06640882b2 100644 --- a/src/REPLICA/fix_event_hyper.cpp +++ b/src/REPLICA/fix_event_hyper.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_event_hyper.h" + #include "comm.h" #include "error.h" #include "update.h" diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index 16c37fcb77eb430f20ac93350934e1835889f40d..f104d14c2f0f76b379d23b70596b26a20d02f6c1 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_hyper_global.h" -#include + #include #include #include "atom.h" diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index 9e3ce9b00d6ad8f0c53d4ad130d7310fb5609ecb..e57419022ccb72a6c07ab5be03a090ad9af58c1d 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_hyper_local.h" -#include + #include #include -#include + #include "atom.h" #include "update.h" #include "group.h" @@ -30,7 +30,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index 30683052325b57765e30da368f64f013cb45e4e9..b8fd0f64428771463f39a43ce7c9ef130dcc3c74 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -17,22 +17,21 @@ ------------------------------------------------------------------------- */ #include "fix_neb.h" -#include -#include -#include -#include -#include "universe.h" -#include "update.h" + #include "atom.h" -#include "domain.h" #include "comm.h" -#include "modify.h" #include "compute.h" -#include "group.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "force.h" +#include "group.h" #include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 1e78326fbde9be16bf17dadb116b2171e17392ca..6c4cba4ab8a1f535926c8c5cb2a42f135c191bce 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -12,28 +12,25 @@ ------------------------------------------------------------------------- */ #include "hyper.h" -#include -#include -#include -#include "update.h" + +#include "compute_event_displace.h" #include "domain.h" -#include "region.h" +#include "dump.h" +#include "error.h" +#include "finish.h" +#include "fix_event_hyper.h" +#include "fix_hyper.h" #include "integrate.h" +#include "memory.h" #include "min.h" -#include "force.h" -#include "neighbor.h" #include "modify.h" -#include "compute_event_displace.h" -#include "fix_hyper.h" -#include "fix_event_hyper.h" +#include "neighbor.h" #include "output.h" -#include "dump.h" -#include "finish.h" +#include "region.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 34b5cf40fed828cfa8c8f7cb2fae4be6c10e1570..2d1dd6eea756286862952964d923a2192141c5ca 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -12,28 +12,26 @@ ------------------------------------------------------------------------- */ #include "neb.h" -#include -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "domain.h" #include "comm.h" -#include "min.h" -#include "modify.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" #include "fix_neb.h" +#include "math_const.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "math_const.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 796cf01681f8b9473b08cb7919e5758245f89fec..cdb1eb9b029b003cc1cce0a35aa425fbb0e2bff7 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -16,32 +16,29 @@ ------------------------------------------------------------------------- */ #include "prd.h" -#include -#include -#include -#include "universe.h" -#include "update.h" + #include "atom.h" -#include "domain.h" -#include "region.h" #include "comm.h" -#include "velocity.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix_event_prd.h" #include "integrate.h" +#include "memory.h" #include "min.h" -#include "neighbor.h" #include "modify.h" -#include "compute.h" -#include "fix.h" -#include "fix_event_prd.h" -#include "force.h" -#include "random_park.h" -#include "random_mars.h" +#include "neighbor.h" #include "output.h" -#include "finish.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" +#include "velocity.h" + +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index fba753d602fedd843e10608a9d7a6e53fe0be305..db74b63c35341bc94c46e9002cf726a0cd54c66b 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -16,28 +16,28 @@ ------------------------------------------------------------------------- */ #include "tad.h" -#include -#include -#include -#include "universe.h" -#include "update.h" + #include "atom.h" +#include "compute.h" #include "domain.h" +#include "error.h" +#include "finish.h" +#include "fix_event_tad.h" +#include "fix_store.h" +#include "force.h" #include "integrate.h" +#include "memory.h" #include "min.h" -#include "neighbor.h" #include "modify.h" #include "neb.h" -#include "compute.h" -#include "fix_event_tad.h" -#include "fix_store.h" -#include "force.h" +#include "neighbor.h" #include "output.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index a7ad4c068b465eb20e9eb028127121607bbbf9ac..0cce389bf0a0069770a73f09ec988439c4f23ea8 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -16,22 +16,23 @@ ------------------------------------------------------------------------- */ #include "temper.h" -#include -#include -#include "universe.h" -#include "domain.h" + #include "atom.h" -#include "update.h" -#include "integrate.h" -#include "modify.h" #include "compute.h" -#include "force.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" +#include "force.h" +#include "integrate.h" +#include "modify.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp index 03119d304eac86947777f44bb64fd9136a73abde..03b79cc75008620d654b4a9a434b7a915bda6dfb 100644 --- a/src/RIGID/fix_ehex.cpp +++ b/src/RIGID/fix_ehex.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include "fix_ehex.h" -#include + #include #include #include "atom.h" diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp index ff31ab97559e5fd14c322edcff46f3696ad739de..436b2191ff8fac1bcbfe314c056422252e5a0fd0 100644 --- a/src/RIGID/fix_rattle.cpp +++ b/src/RIGID/fix_rattle.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_rattle.h" -#include + #include #include #include "atom.h" diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 761b9572928de6b28fa1eee243510c9135bf21a5..f74cce82334608022bca0e67b286a7f2072c285a 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid.h" -#include + #include -#include + #include #include "math_extra.h" #include "atom.h" @@ -35,8 +35,8 @@ #include "memory.h" #include "error.h" #include "rigid_const.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp index 5b75640549a74222612277489256f0140f5dedf4..d1204e2bbc4e4d051f972d6b9dc37c1c79ad7149 100644 --- a/src/RIGID/fix_rigid_nh_small.cpp +++ b/src/RIGID/fix_rigid_nh_small.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_nh_small.h" -#include + #include #include #include "math_extra.h" diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 01dd9e889e3647b41d6ae7411b03c7f50cec72e0..85cadc826ed441c8a417dea7d12fe363f9d31b5e 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_rigid_small.h" -#include + #include -#include + #include #include #include "math_extra.h" @@ -39,8 +39,8 @@ #include "memory.h" #include "error.h" #include "rigid_const.h" -#include "utils.h" -#include "fmt/format.h" + + #include diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp index d6603cd7b66cad47bea72ba9c0da82175e82b92c..ee88f57341ae0f5b26b042e333ec8fdbe8811516 100644 --- a/src/RIGID/fix_shake.cpp +++ b/src/RIGID/fix_shake.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_shake.h" -#include + #include #include #include @@ -32,8 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp index b5b586bc7f784af07d719440067651076602ac0c..509e45202ca4b14292d192f6fef68ed85f22eb21 100644 --- a/src/SHOCK/fix_append_atoms.cpp +++ b/src/SHOCK/fix_append_atoms.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_append_atoms.h" -#include + #include #include #include "atom.h" diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp index 986b1323e81803c7ac93a9b8a153031f422b037a..3930133221d91b5a25caa1229921753b05ae9d28 100644 --- a/src/SHOCK/fix_msst.cpp +++ b/src/SHOCK/fix_msst.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_msst.h" -#include + #include #include #include "atom.h" @@ -32,8 +32,8 @@ #include "domain.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp index 1e85441d1f02278b1d90077b952da63f66de2df7..37b82b86f0fea468428ae303051e1bff4e41f01f 100644 --- a/src/SNAP/compute_sna_atom.cpp +++ b/src/SNAP/compute_sna_atom.cpp @@ -13,7 +13,7 @@ #include "compute_sna_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp index 13761930705b10431ab2a2d82a6055d1c21451b2..bb546708b84a0c1010ca7bdb12e1775e53fc0438 100644 --- a/src/SNAP/compute_snad_atom.cpp +++ b/src/SNAP/compute_snad_atom.cpp @@ -13,7 +13,7 @@ #include "compute_snad_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snap.cpp b/src/SNAP/compute_snap.cpp index eb18b7274e9470e2241ab9dc32111ff7cff5cb94..ca989a75b41cfd13529d6cfe229d862f5a94612b 100644 --- a/src/SNAP/compute_snap.cpp +++ b/src/SNAP/compute_snap.cpp @@ -13,7 +13,7 @@ #include "compute_snap.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp index 066fc56c119be7bf058ef769f30dda55824c522e..dd562cac5c84285730bb7318cf9413ec6999dbff 100644 --- a/src/SNAP/compute_snav_atom.cpp +++ b/src/SNAP/compute_snav_atom.cpp @@ -13,7 +13,7 @@ #include "compute_snav_atom.h" #include -#include + #include "sna.h" #include "atom.h" #include "update.h" diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 48014592edb5932077e61c1df48e006749d40e3a..cb1a71aa453849b119412fe5f850cd5546461ecd 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "pair_snap.h" -#include + #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "sna.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index 94eff27f5357e08e541be9aeeae989bd26f41aec..281100740aadd5f2c6d4f9a0ddc9609f2cc0d341 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "compute_spin.h" -#include + #include #include #include "atom.h" diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 6df9dd4af290bb3722807e0740da070c7dad2450..82bf83ac10342b9a222d0ffe1b352226ac2b4030 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -34,7 +34,7 @@ #include "random_mars.h" #include "respa.h" #include "update.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/SPIN/fix_neb_spin.cpp b/src/SPIN/fix_neb_spin.cpp index 110cfb58d8ad5482addf3b9485747afaea43e38d..0b2e86e4656c1858bd4489fc129911a00f91af91 100644 --- a/src/SPIN/fix_neb_spin.cpp +++ b/src/SPIN/fix_neb_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_neb_spin.h" -#include + #include #include #include "universe.h" diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index 9a33f0d61de054062d252c1168904260d034b44e..cbb367e43866814b1ad7d58015d2b800ce182efb 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_precession_spin.h" -#include + #include #include #include "atom.h" diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp index df7fc71f8b48968834f4a71efaf77384ed6b4879..f36f11f2a9eecf641587dd3e2fbcd0d73dcbc5e5 100644 --- a/src/SPIN/min_spin.cpp +++ b/src/SPIN/min_spin.cpp @@ -18,17 +18,17 @@ ------------------------------------------------------------------------- */ #include "min_spin.h" -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "output.h" -#include "timer.h" #include "error.h" #include "math_const.h" +#include "output.h" +#include "timer.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/min_spin_cg.cpp b/src/SPIN/min_spin_cg.cpp index a658713d1bdab1bfaeb8d39c1e344667288dfd38..4b8b74541940c270212b19232a88c3ba47c25cdf 100644 --- a/src/SPIN/min_spin_cg.cpp +++ b/src/SPIN/min_spin_cg.cpp @@ -21,25 +21,22 @@ preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "min_spin_cg.h" -#include "universe.h" + #include "atom.h" #include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" +#include "math_const.h" +#include "memory.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "memory.h" -#include "modify.h" -#include "math_special.h" -#include "math_const.h" #include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/min_spin_lbfgs.cpp b/src/SPIN/min_spin_lbfgs.cpp index f92fc69e0497439c3e8c657f0f9e5caae8016aa8..40029b7e7179ded12b62457950344d53d68eeb56 100644 --- a/src/SPIN/min_spin_lbfgs.cpp +++ b/src/SPIN/min_spin_lbfgs.cpp @@ -21,24 +21,22 @@ preprint arXiv:1904.02669. ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "min_spin_lbfgs.h" + #include "atom.h" #include "citeme.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" +#include "math_const.h" +#include "memory.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "memory.h" -#include "modify.h" -#include "math_special.h" -#include "math_const.h" #include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index 96808b7f104e3fb69e12e3147339db14d1f04720..a89ca403cedb2fa38737ecf27030132dd3aa2f1b 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -22,29 +22,26 @@ ------------------------------------------------------------------------- */ #include "neb_spin.h" -#include -#include -#include -#include -#include "citeme.h" -#include "force.h" -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "domain.h" +#include "citeme.h" #include "comm.h" -#include "min.h" -#include "modify.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" #include "fix_neb_spin.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "output.h" #include "thermo.h" -#include "finish.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_dipole_cut.cpp b/src/SPIN/pair_spin_dipole_cut.cpp index 5573d914b73f1ffab1ec9215a662a602814a263a..b27c9736b2ab4a8adba741182ae32e7cc1deeb29 100644 --- a/src/SPIN/pair_spin_dipole_cut.cpp +++ b/src/SPIN/pair_spin_dipole_cut.cpp @@ -22,20 +22,17 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dipole_cut.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "fix.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "memory.h" -#include "modify.h" -#include "error.h" -#include "update.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dipole_long.cpp b/src/SPIN/pair_spin_dipole_long.cpp index 4188bb214ce8f5b1fd01141ba90c1c72d4a4cf79..d4b1b8e43ea75791565402b7e14c63828298f058 100644 --- a/src/SPIN/pair_spin_dipole_long.cpp +++ b/src/SPIN/pair_spin_dipole_long.cpp @@ -17,21 +17,18 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dipole_long.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "fix.h" +#include "error.h" #include "force.h" #include "kspace.h" #include "math_const.h" #include "memory.h" -#include "modify.h" -#include "error.h" -#include "update.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index b4b3fcb6f586ae888cd3b49cef24e76373ea320a..e27f9fad7dd57b19d4533a69084a28d816a4efae 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -22,19 +22,16 @@ ------------------------------------------------------------------------- */ #include "pair_spin_dmi.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "fix.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index b82dca3dcc8c3a34930b4810cea77a08f17f6261..27da47dd0f782e8262a87ad884da6a434fde6e14 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -22,19 +22,16 @@ ------------------------------------------------------------------------- */ #include "pair_spin_exchange.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 50cd1fe54ae9c6b5cc88e0913ee5158842ec4593..2242cf985d5bbfdc008ca8b81b3226f1e5cfe103 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -22,19 +22,16 @@ ------------------------------------------------------------------------- */ #include "pair_spin_magelec.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 4468e157b42cee3b3b970de701422fd0d3ba0393..33ea904c0c5eef43d94fe373c826877aa72b1659 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -22,19 +22,16 @@ ------------------------------------------------------------------------- */ #include "pair_spin_neel.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "error.h" -#include "fix.h" #include "force.h" -#include "neigh_list.h" #include "memory.h" -#include "modify.h" -#include "update.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index ca0bdbac0a75a7f77ee18b2c8ef9fdf12d71fb2a..688522c1bdb68ce2ff8e9382399e4b1c4a38d9a9 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_srd.h" -#include + #include #include #include "math_extra.h" diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp index 8b9ea6fb795d99a26755e4eb216f12500913d158..8ffd764447b400efdc70466c3487304999815843 100644 --- a/src/SRD/fix_wall_srd.cpp +++ b/src/SRD/fix_wall_srd.cpp @@ -12,18 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_wall_srd.h" -#include -#include -#include "fix.h" + #include "domain.h" -#include "lattice.h" +#include "error.h" +#include "fix.h" #include "input.h" +#include "lattice.h" +#include "memory.h" #include "modify.h" #include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp index 2165132856446f0f53d750f0d1b01eb0242830bc..dd02676466df5927ae668810391bcc24cbd889a3 100644 --- a/src/USER-ATC/fix_atc.cpp +++ b/src/USER-ATC/fix_atc.cpp @@ -12,23 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_atc.h" -#include -#include -#include -#include "fix_nve.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "pointers.h" #include "comm.h" +#include "error.h" #include "group.h" +#include "neigh_request.h" +#include "neighbor.h" #include "ATC_Method.h" -#include "ATC_Transfer.h" #include "ATC_TransferKernel.h" #include "ATC_TransferPartitionOfUnity.h" #include "ATC_CouplingEnergy.h" @@ -37,6 +29,8 @@ #include "ATC_CouplingMomentumEnergy.h" #include "LammpsInterface.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; using std::string; diff --git a/src/USER-ATC/fix_atc.h b/src/USER-ATC/fix_atc.h index 2512c658dbc7b7cff2113107bef7c94621e618da..5bf26f6eaac23f18b5b93229f2d89237c153ce64 100644 --- a/src/USER-ATC/fix_atc.h +++ b/src/USER-ATC/fix_atc.h @@ -8,7 +8,6 @@ FixStyle(atc,FixATC) #define FIX_ATC_H #include "fix.h" -#include "pointers.h" // access to lammps pointers namespace ATC { class ATC_Method; diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp index 0d11e983ad1fba606ed42b44f8a346abe0b0e193..46b239be08c31a0c5a9d1690bf06010d5f27055e 100644 --- a/src/USER-AWPMD/atom_vec_wavepacket.cpp +++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp @@ -16,9 +16,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_wavepacket.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp index 2aa2e7680b2aff32a909b6f31bbfdd0c24a886ed..178f0f42defdbda188e7ef6e67bb90864f2f7635 100644 --- a/src/USER-AWPMD/fix_nve_awpmd.cpp +++ b/src/USER-AWPMD/fix_nve_awpmd.cpp @@ -22,7 +22,7 @@ #include "update.h" #include "respa.h" #include "error.h" -#include "utils.h" + #include "TCP/wpmd_split.h" diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 4d812852db2af93f1b0da333420e5664225c8af3..5e23b7fc69df54eeb5e6d0ead09dfa289b0c4a04 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -16,29 +16,30 @@ ------------------------------------------------------------------------- */ #include "pair_awpmd_cut.h" -#include -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "min.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" +#include "memory.h" +#include "min.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" +#include "update.h" #include "logexc.h" #include "vector_3.h" #include "TCP/wpmd.h" #include "TCP/wpmd_split.h" +#include +#include +#include +#include +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -237,7 +238,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) etmap[etag[i]].push_back(i); } else - error->all(FLERR,fmt("Invalid spin value (%d) for particle %d !",spin[i],i)); + error->all(FLERR,logfmt("Invalid spin value (%d) for particle %d !",spin[i],i)); } // ion force vector Vector_3 *fi=NULL; @@ -254,7 +255,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) for(size_t k=0;kall(FLERR,fmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i)); + error->all(FLERR,logfmt("WP splits for one electron should have the same spin (at particles %d, %d)!",el[0],i)); double m= atom->mass ? atom->mass[type[i]] : force->e_mass; Vector_3 xx=Vector_3(x[i][0],x[i][1],x[i][2]); Vector_3 rv=m*Vector_3(v[i][0],v[i][1],v[i][2]); diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp index 39da9fc23b27bd1bd74a01808df493216ee22b61..a4b8de84bd518bc055839864bdf8f546bf4a3b9d 100644 --- a/src/USER-BOCS/compute_pressure_bocs.cpp +++ b/src/USER-BOCS/compute_pressure_bocs.cpp @@ -16,11 +16,6 @@ #include "compute_pressure_bocs.h" -#include -#include -#include -#include - #include "angle.h" #include "atom.h" #include "bond.h" @@ -28,15 +23,15 @@ #include "domain.h" #include "error.h" #include "fix.h" -#include "fmt/format.h" #include "force.h" #include "improper.h" #include "kspace.h" -#include "memory.h" #include "modify.h" #include "pair.h" #include "update.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index c61a37388b02215732fea25366a50aaa01d81b60..6f7962c83f6a0fad379c78de50c2e55d7d63e054 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -17,7 +17,7 @@ #include "fix_bocs.h" #include -#include + #include #include @@ -29,7 +29,7 @@ #include "domain.h" #include "error.h" #include "fix_deform.h" -#include "fmt/format.h" + #include "force.h" #include "group.h" #include "irregular.h" diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index cc70f2fb31015574bc4c7c9a7e4a9b6e60bbed93..c9540bf0c070152b7a35b3201c2eb1f45cda31aa 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "bond_oxdna_fene.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/bond_oxrna2_fene.cpp b/src/USER-CGDNA/bond_oxrna2_fene.cpp index bdddccda87f8586f6ef58ae1806fb59e2e010ff5..2dee1224d3a5a1c4054659906c458e3c25aea851 100644 --- a/src/USER-CGDNA/bond_oxrna2_fene.cpp +++ b/src/USER-CGDNA/bond_oxrna2_fene.cpp @@ -14,8 +14,6 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include #include "bond_oxrna2_fene.h" using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp index 66871fa64e97a14f5321b27a0403b7b57201d062..17b1fb7b42905ee43257fee5f6d8b4ce904dacd2 100644 --- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp +++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp @@ -16,16 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_nve_dotc_langevin.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "force.h" -#include "update.h" #include "comm.h" -#include "random_mars.h" #include "error.h" +#include "math_extra.h" +#include "random_mars.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index 32ee0ed1451d5f2faa031f6265ca54ca9fec4712..662d55c5900cbe93e68da92d668ed6cc98af6c2f 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -15,21 +15,20 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_coaxstk.h" -#include -#include -#include -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index 04aaf82ccbdd7f4a3b465ba54bf4c4b1c9c72746..f23ca4fbf71417fe5df67a4d186c9c4f156b48de 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -15,19 +15,18 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna2_dh.h" -#include -#include -#include + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" +#include "force.h" #include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index 87f58857bbae514f5b1e8a0f54e3e2a2cfc985bb..f1d425a0b3bd7f7654e57be60cbb4c06c43e1bad 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -15,21 +15,20 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_coaxstk.h" -#include -#include -#include -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 22ed31000382f19cfc7c1e25acc3df105d296d2b..ad96186b6bb247dff90d79d57482319403c88c02 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -15,20 +15,19 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_excv.h" -#include -#include -#include -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" +#include "force.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MFOxdna; diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index df952d0ff26871fe74d7a6b6ba76438e593ed0e6..7987210d7acc74c8e0bdd0a3f88fead487269f91 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -15,20 +15,19 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_hbond.h" -#include -#include -#include -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" +#include "force.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MFOxdna; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index fa9204ed86ce0d127414b20cd208ea0ae0a52038..bf52d61182b1f6441e870975aa694a0bfc378c21 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_stk.h" -#include + #include #include #include @@ -26,7 +26,7 @@ #include "neighbor.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "atom_vec_ellipsoid.h" #include "math_extra.h" diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index 7845451dafa1141140aee9f14bc215ec3f4d2e2d..17514996832283a637c8dbf26fd22e0568407321 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -15,21 +15,20 @@ ------------------------------------------------------------------------- */ #include "pair_oxdna_xstk.h" -#include -#include -#include -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxrna2_excv.cpp b/src/USER-CGDNA/pair_oxrna2_excv.cpp index 3c0194d636d9b4335f3dc8d105a4a28c8b80071f..af9fdaaaa17513ee95ea4918e4855c9ea03ea3da 100644 --- a/src/USER-CGDNA/pair_oxrna2_excv.cpp +++ b/src/USER-CGDNA/pair_oxrna2_excv.cpp @@ -14,12 +14,10 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxrna2_excv.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-CGDNA/pair_oxrna2_stk.cpp b/src/USER-CGDNA/pair_oxrna2_stk.cpp index 1b6c577a19b73330f28d3268ba6a0c1c9b700fb7..fd02946134ec6e59200365602583eac1ad4544bd 100644 --- a/src/USER-CGDNA/pair_oxrna2_stk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_stk.cpp @@ -14,26 +14,22 @@ Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_oxrna2_stk.h" -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" #include "math_const.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neighbor.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGDNA/pair_oxrna2_xstk.cpp b/src/USER-CGDNA/pair_oxrna2_xstk.cpp index 11c2f2b9b13e09087bb6f971a6c1bce0e89bdd14..673ef1c9a38c0e927340c4a93a69f75234561203 100644 --- a/src/USER-CGDNA/pair_oxrna2_xstk.cpp +++ b/src/USER-CGDNA/pair_oxrna2_xstk.cpp @@ -15,21 +15,20 @@ ------------------------------------------------------------------------- */ #include "pair_oxrna2_xstk.h" -#include -#include -#include -#include "mf_oxdna.h" + #include "atom.h" +#include "atom_vec_ellipsoid.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "atom_vec_ellipsoid.h" #include "math_extra.h" +#include "memory.h" +#include "mf_oxdna.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index d535baeda5dea824f364a417f58c61153cca431c..6f97d2104ff1c8301c23fb946280c2c3bd77112c 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "angle_sdk.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "lj_sdk_common.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index cf478e85fbcfd1a0af97e9d1d974a9f9a6bb95a4..8185e2487665f27b29530d054298f0291b2e24bd 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" diff --git a/src/USER-CGSDK/pair_lj_sdk.h b/src/USER-CGSDK/pair_lj_sdk.h index ef0263c06bed225b0f13b658b6291e3829a83b68..11c123a72c87a3f04fe325b375a7d761c4919d53 100644 --- a/src/USER-CGSDK/pair_lj_sdk.h +++ b/src/USER-CGSDK/pair_lj_sdk.h @@ -27,7 +27,6 @@ PairStyle(lj/sdk,PairLJSDK) #include "pair.h" namespace LAMMPS_NS { -class LAMMPS; class PairLJSDK : public Pair { public: diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index cd02c7f9e1c70d2c5ae07ef6a4f7d69feb20b344..42f1ff3ce7f4329a779db41f7994297a1e6521e4 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sdk_coul_long.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #define LMP_NEED_SDK_FIND_LJ_TYPE 1 #include "lj_sdk_common.h" diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp index f9e071a0b384eafe94514434ae45324ad4bdecf4..fcbfb58456e6d6d2753eac6c312b94741f3267cb 100644 --- a/src/USER-COLVARS/fix_colvars.cpp +++ b/src/USER-COLVARS/fix_colvars.cpp @@ -25,29 +25,26 @@ ------------------------------------------------------------------------- */ #include "fix_colvars.h" -#include -#include -#include -#include -#include -#include -#include #include "atom.h" +#include "citeme.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "force.h" #include "memory.h" #include "modify.h" #include "respa.h" #include "universe.h" #include "update.h" -#include "citeme.h" #include "colvarproxy_lammps.h" #include "colvarmodule.h" +#include +#include +#include +#include + static const char colvars_pub[] = "fix colvars command:\n\n" "@Article{fiorin13,\n" diff --git a/src/USER-COLVARS/fix_colvars.h b/src/USER-COLVARS/fix_colvars.h index 2486446f3546d13163613e5aac0a072d377052b3..fff61ce218baff81bc4e4416321d36f07555f3ec 100644 --- a/src/USER-COLVARS/fix_colvars.h +++ b/src/USER-COLVARS/fix_colvars.h @@ -34,7 +34,6 @@ FixStyle(colvars,FixColvars) #define LMP_FIX_COLVARS_H #include "fix.h" -#include class colvarproxy_lammps; diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 1e37e2de9c9d7be83da409b65d0500acb86eed85..07a8ac2d5c332f3b10c15e759f4790113a71aae9 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -17,12 +17,11 @@ ------------------------------------------------------------------------- */ #include "group_ndx.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "group.h" #include "error.h" +#include "group.h" using namespace LAMMPS_NS; diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp index feab2f22b283d08ca983cd90deb202f0b51be967..bab1592b1ecd728825625774c5cffd713ae5eb76 100644 --- a/src/USER-COLVARS/ndx_group.cpp +++ b/src/USER-COLVARS/ndx_group.cpp @@ -17,13 +17,13 @@ ------------------------------------------------------------------------- */ #include "ndx_group.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "group.h" #include "error.h" +#include "group.h" + +#include using namespace LAMMPS_NS; #define BUFLEN 4096 diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 5dd47b28bd4c86618a32de0847f39c637f2db1df..d16fbf2876335c730b1949a1f3fc310b02324bf7 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -15,23 +15,23 @@ Contributing authors: Shawn Coleman & Douglas Spearot (Arkansas) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "compute_saed.h" -#include -#include -#include -#include -#include "math_const.h" -#include "compute_saed_consts.h" + #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "update.h" +#include "compute_saed_consts.h" #include "domain.h" +#include "error.h" #include "group.h" -#include "citeme.h" +#include "math_const.h" #include "memory.h" -#include "error.h" +#include "update.h" +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index e75546b5483a5fdfa83bbb67f18db401fbe46efb..b48de49c81731d0b78c61c1c6ea3eb10b560b218 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -16,23 +16,23 @@ Updated: 06/17/2015-2 ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "compute_xrd.h" -#include -#include -#include -#include -#include "math_const.h" #include "compute_xrd_consts.h" + #include "atom.h" +#include "citeme.h" #include "comm.h" -#include "update.h" #include "domain.h" +#include "error.h" #include "group.h" -#include "citeme.h" +#include "math_const.h" #include "memory.h" -#include "error.h" +#include "update.h" +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 0a018338a464c627b96a765273cb43bd50d0612a..39382264c46af74d97516ce15650b235a7f8dc85 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -17,18 +17,17 @@ ------------------------------------------------------------------------- */ #include "fix_saed_vtk.h" -#include -#include -#include -#include "update.h" -#include "modify.h" + #include "compute.h" #include "compute_saed.h" -#include "memory.h" -#include "error.h" -#include "force.h" #include "domain.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/compute_dpd.cpp b/src/USER-DPD/compute_dpd.cpp index 0ef78681646d61578e76df265788d413f454b6f3..97e12d5cb4b90ded6472605ca4cdf03f5837ab08 100644 --- a/src/USER-DPD/compute_dpd.cpp +++ b/src/USER-DPD/compute_dpd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_dpd.h" -#include + #include "atom.h" #include "update.h" #include "error.h" diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp index bd0e334ffcd7ed8024f314da653bb9be8c540cf0..db9b877b1cd3bc0264c5665669232fe64560ead0 100644 --- a/src/USER-DPD/fix_eos_cv.cpp +++ b/src/USER-DPD/fix_eos_cv.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "fix_eos_cv.h" + #include "atom.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp index 69e53369457703f0edf73edebade141e53c7b61b..57cfe03dc8dd1eac7bbdd2ae321efcaf2b1edeb1 100644 --- a/src/USER-DPD/fix_eos_table.cpp +++ b/src/USER-DPD/fix_eos_table.cpp @@ -16,14 +16,12 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table.h" -#include -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" #include "memory.h" -#include "utils.h" + +#include #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp index d728f7e98737db50bd4598b2395ead089d08fc69..c220d84a576954a9337af36797ceac0a6e2e2e9b 100644 --- a/src/USER-DPD/fix_eos_table_rx.cpp +++ b/src/USER-DPD/fix_eos_table_rx.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "fix_eos_table_rx.h" -#include -#include + + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "memory.h" #include "comm.h" #include "modify.h" -#include "utils.h" + #define MAXLINE 1024 diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index ced7283ef401b902f4465949109ba607a565fcd1..d974d12473d471ee0a3b023dae4ff835f6d61da0 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_rx.h" -#include -#include + + #include #include #include // DBL_EPSILON @@ -31,7 +31,7 @@ #include "neigh_request.h" #include "math_special.h" #include "pair_dpd_fdt_energy.h" -#include "utils.h" + #include // std::vector<> #include // std::max diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 18c86976ac266363ab9479b1c25f48b5b625dacf..c4480a037334c1ba3bffb47bbe457fdb0df01df5 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -34,27 +34,26 @@ ------------------------------------------------------------------------- */ #include "fix_shardlow.h" -#include -#include -#include -#include + #include "atom.h" -#include "force.h" -#include "update.h" -#include "error.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "npair.h" -#include "memory.h" -#include "domain.h" -#include "modify.h" +#include "npair_half_bin_newton_ssa.h" #include "pair_dpd_fdt.h" #include "pair_dpd_fdt_energy.h" -#include "npair_half_bin_newton_ssa.h" -#include "citeme.h" -#include "utils.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 876d76a42f971f9d68bb145ab3349de76e49a9d5..1d3d952e9f2040a36f2a6ec983400c3f01fee786 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -16,21 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_fdt.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" #include "memory.h" #include "modify.h" -#include "error.h" -#include "utils.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 3686bcb7e93b3ee01df0e8297757d031c584b251..b843e4601af48c5227ef6bcb2933da61cf42587b 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -16,21 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_fdt_energy.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "random_mars.h" #include "memory.h" #include "modify.h" -#include "error.h" -#include "utils.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "random_mars.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 839d22b50b32c18f80751665828eb8152441bb69..666a1b0ea95d58d4bb0afedf68f76174317cac85 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "pair_exp6_rx.h" -#include + #include -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "modify.h" #include "fix.h" diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index f9074d5c056423957c67f829f213bae66c6d2eaf..ceb5c78eaf88853e22c3c7f8425b59b982618997 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -21,10 +21,10 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include + #include #include "math_const.h" -#include + #include #include "pair_multi_lucy.h" #include "atom.h" @@ -33,9 +33,9 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index 90f6dc6170e30b71ebb2b0457415f4a66c26951f..d769d94783b1fcaa6ced3f9872f08d1a838caa28 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -21,10 +21,10 @@ The Journal of Chemical Physics, 2016, 144, 104501. ------------------------------------------------------------------------------------------- */ -#include + #include #include "math_const.h" -#include + #include #include "pair_multi_lucy_rx.h" #include "atom.h" @@ -33,11 +33,11 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" #include "modify.h" #include "fix.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 56c3e28c468eb31cc332702bb45109ec5a9f570f..f791107f1d84909778d1ca8d23720fbf0a9d51a2 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_table_rx.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "error.h" #include "modify.h" #include "fix.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp index a12c248680593046b1f3dca27fd5595484248268..b806b4434bf896b810b83a100e7987d60b861524 100644 --- a/src/USER-DRUDE/compute_temp_drude.cpp +++ b/src/USER-DRUDE/compute_temp_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_drude.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp index 080408459c754863f6f9054a18e98f2791a05a2d..313ac249d7fadb79d612b2542dd621612270b6d5 100644 --- a/src/USER-DRUDE/fix_drude.cpp +++ b/src/USER-DRUDE/fix_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_drude.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp index 4128c508d69fd75a94a793c916f20587a99eb9be..bdccaaebc845c201703c9acd062a868775483f91 100644 --- a/src/USER-DRUDE/fix_drude_transform.cpp +++ b/src/USER-DRUDE/fix_drude_transform.cpp @@ -13,7 +13,7 @@ /** Fix Drude Transform ******************************************************/ #include "fix_drude_transform.h" -#include + #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp index e865e9cd29255d2a457efa6e8b52d0ec605783ec..da745108217ccfac16bbf72671270a8b28e370fd 100644 --- a/src/USER-DRUDE/fix_langevin_drude.cpp +++ b/src/USER-DRUDE/fix_langevin_drude.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin_drude.h" -#include + #include #include #include "fix_drude.h" diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index 875b4a9cbaf883f21935af86a8ab9c01cb7ac0c8..461f972885a1bb01ca029d933ea5c5d1d9811238 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_thole_long.h" -#include + #include #include #include "fix_drude.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "modify.h" #include "domain.h" diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 882fd047a92321ada64837d169bc29a6e996dba7..281317c0764e69bd445c40405861aaee4c8c3528 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_thole.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "fix.h" #include "fix_drude.h" #include "domain.h" diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp index 0912fb0498ace947cd997b1cc256f475cf8c3a6a..65923d2e7517b4d089babdb478903ae240d7e600 100644 --- a/src/USER-EFF/atom_vec_electron.cpp +++ b/src/USER-EFF/atom_vec_electron.cpp @@ -16,10 +16,11 @@ ------------------------------------------------------------------------- */ #include "atom_vec_electron.h" -#include + #include "atom.h" #include "citeme.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp index c943366f1b3f414cc2ff5575347a32cacacdb01e..001e1d4c4309af9c869feb4aa3ffb414645f824d 100644 --- a/src/USER-EFF/compute_ke_atom_eff.cpp +++ b/src/USER-EFF/compute_ke_atom_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "compute_ke_atom_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp index 3e277fc66c4b7e0d2e4ee8acb47bf56f3dc496a9..d1781b75f70001017125088309a796a1708c14ed 100644 --- a/src/USER-EFF/compute_ke_eff.cpp +++ b/src/USER-EFF/compute_ke_eff.cpp @@ -15,8 +15,8 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include -#include + + #include "compute_ke_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index dcf7e8623451bf8d5f0e12b185551df394cc45ec..90e25ca3c813ed08061599161a3378051f12c195 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include -#include + #include "compute_temp_deform_eff.h" #include "domain.h" #include "atom.h" diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp index e9295ea6804606a692aad3b363c16f3724882128..174f032b83c5f9faaaa6c257ef23cbc6a6eb302f 100644 --- a/src/USER-EFF/compute_temp_eff.cpp +++ b/src/USER-EFF/compute_temp_eff.cpp @@ -16,8 +16,8 @@ ------------------------------------------------------------------------- */ #include "compute_temp_eff.h" -#include -#include + + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index b27699cde94b6e655ffd6987e6d62ed5d9d45048..c95cf0de2df4f34f79439bfe5708fada47e7e3f0 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include -#include + #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp index 5158d7c68122c0ef55357df370f287818256ef2f..3966bc7b9847315263d15b9cc597809bad4263a7 100644 --- a/src/USER-EFF/fix_langevin_eff.cpp +++ b/src/USER-EFF/fix_langevin_eff.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include + #include -#include + #include "fix_langevin_eff.h" #include "atom.h" #include "update.h" diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp index 034233732ec7b415adbf1fcc44b7a1fa40f13788..d5b574510c4f146f3db58c3b36fbe06e2bb11d46 100644 --- a/src/USER-EFF/fix_nh_eff.cpp +++ b/src/USER-EFF/fix_nh_eff.cpp @@ -15,10 +15,10 @@ Contributing author: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ -#include + #include "fix_nh_eff.h" + #include "atom.h" -#include "atom_vec.h" #include "error.h" #include "domain.h" diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp index ea719c91c02f6592bd445cff4f17818ecc85e0ee..f32a45fd469019ddc99fa21fdefb3a6bd63dd20a 100644 --- a/src/USER-EFF/fix_nve_eff.cpp +++ b/src/USER-EFF/fix_nve_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include "fix_nve_eff.h" #include "atom.h" #include "force.h" diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 0ebbf04d642a93fe82cf54319c5a87a649728848..02a463b3ba3d5300320bcae072f33c02f9fe3f27 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -13,7 +13,7 @@ #include #include -#include + #include "fix_nvt_sllod_eff.h" #include "math_extra.h" #include "atom.h" diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp index e2163990bd999cf865781dee2bf152b8323545cb..a013270049ad870e389652cb0716fc66f48d0f4a 100644 --- a/src/USER-EFF/fix_temp_rescale_eff.cpp +++ b/src/USER-EFF/fix_temp_rescale_eff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_temp_rescale_eff.h" #include "atom.h" diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index b9b442ed2af21673efbfb033d9a638c8f6253b2c..f4e7af65848b404c23068bfb0ec1bc42a58fed85 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -15,9 +15,9 @@ Contributing author: Andres Jaramillo-Botero ------------------------------------------------------------------------- */ -#include + #include -#include + #include #include "pair_eff_cut.h" #include "pair_eff_inline.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp index 488a85fc209bd2c610e04d3b6b9b7df7230772ff..ff1e303a305290f10aea1cc51c1c3c028aa6cfc9 100644 --- a/src/USER-FEP/compute_fep.cpp +++ b/src/USER-FEP/compute_fep.cpp @@ -18,7 +18,7 @@ #include "compute_fep.h" #include #include -#include + #include "comm.h" #include "update.h" #include "atom.h" @@ -34,7 +34,7 @@ #include "timer.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp index f88f2b6c40ea0859c4f4e235962f66ee437106d1..2f97b5a0e381c415eee6177435610bc6f70ba4cb 100644 --- a/src/USER-FEP/fix_adapt_fep.cpp +++ b/src/USER-FEP/fix_adapt_fep.cpp @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index fd5141525c43c45437a681f4e9d4d40828b85199..b0a099a56f0b8c1cbb5314d29b3a5e9dd5257ac8 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index 39e06ddd60ca96c3c634d1cfc3d5d281cbae1af4..80173f3f0f9fafe51897646ef17b9a3b74858ca6 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index f9149c8fb8330e100ce1202d39fbd73a2e86c5d4..e13b98329f971e1ad28de2c3f44874490a1a885a 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_charmm_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp index f1aa99b416e6b20e82205429526d99b8cb3f6c42..bfd5a630f67657cfe36048cd788ca41cdcad6ed2 100644 --- a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp index 19c41f04cb1bc03630ccee9b3e3746b6e4e0ea79..e027a3018548f4bfb58d070a1b1f0d46af4a697a 100644 --- a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp index 3c1869da0848f410c626d1d6efe1c9abef08e404..0cd1fc9e87f97b751c728ce3e4dc216a7c692801 100644 --- a/src/USER-FEP/pair_lj_class2_soft.cpp +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_class2_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index 4a92a6fcef6403241b0ccc8b8e2d85ba6d28e68b..a18256f98a79becd1ff8bc4bef4e6b4e250756eb 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut_soft.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index 56cf31b9d33778176daebb499a18cea269a70f32..4b3fae77b37aa9167780bef606f615f49db3ba69 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_long_soft.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index 2ab677c454c68e4831564d79bb9c6388bb7e38c0..786715d6c992f87582642feb77fc8d353e5c4d13 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_soft.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 35342f68d805319992ee89ee98ca8d52cfacf0f4..18f8db5021580f451192588491133eebda55d1b2 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_tip4p_long_soft.h" -#include + #include #include #include "angle.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 904799e1d39e8973f39974a071fa9aa43964260b..85a30a5414fb2fe1c7d14acfa2565b8501f782a6 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index fa130a9dc639300a5160a1818e05c7f8b5917162..9578befd3785146577286b1fd29cd25659ab5ca1 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_tip4p_long_soft.h" -#include + #include #include #include "angle.h" @@ -31,7 +31,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 0c07e844cbc1baf6876e4eba8d8c7e07476a15ab..e9daf71867dc811722464750d25820ca4cc8923f 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include #include "ch5md.h" diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index 9275e82f1c98528d1f02efb9aa52d92e27d1400f..7aad7f754a09060cca9586ee7c7cc7dfd37f5a66 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -15,20 +15,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "angle_charmm_intel.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "modify.h" #include "math_const.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 49a71038dafcba324da350dcdffcd7247b50e08d..290f7320b13932e1d0d58c8c93d7187438bf646f 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -15,20 +15,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "angle_harmonic_intel.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "modify.h" #include "math_const.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index 5c58e7bf10f08b5a03a6f9d4176fa1841a066d85..6b458aeefb1e091ffd9cda86298dfa22ac99107a 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -15,19 +15,21 @@ Contributing author: Stan Moore (Sandia) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include + #include "bond_fene_intel.h" + #include "atom.h" -#include "modify.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 8bf0a82218562f9148d18f77addbbc86e6e76d14..84d94b8f3d86f42a5fa5241ac2c44b1b867051e3 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -15,19 +15,20 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "bond_harmonic_intel.h" + #include "atom.h" -#include "modify.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp index 61fc1dfbd548a77d1baffbca8f4bba19216db5ea..ddfa0c122807ce9523f85879435bf9e32070f463 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/USER-INTEL/dihedral_charmm_intel.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include + #include #include "dihedral_charmm_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index fb8051474e64453ce8fa7e2257468a0902eec9dc..67b82b62bf01cea76ad5c9addcec60e970ed2882 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "dihedral_fourier_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" +#include "suffix.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index f6c4ea0fdeb7425095c839a7590c8a6b0489f40e..ea9bc33c57d4654b504f8535f1a11bc2244e3624 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "dihedral_harmonic_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" +#include "suffix.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 79a8874a722c044061c87f9283188eb2ac3dc979..fa8fd53defac5e15ad6a4aead4f356d06669b06b 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "dihedral_opls_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" +#include "force.h" #include "memory.h" #include "modify.h" #include "neighbor.h" -#include "domain.h" -#include "force.h" -#include "pair.h" +#include "suffix.h" #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; #define PTOLERANCE (flt_t)1.05 diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index 7bd510b1899d1d9026179bc46d79459c4b4a05d5..eacbc7ddcc2b2531845cb4db9977d46ae4c36b9f 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -16,8 +16,8 @@ Anupama Kurpad (Intel) - Host Affinitization ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_intel.h" + #include "comm.h" #include "error.h" #include "force.h" @@ -25,16 +25,9 @@ #include "neigh_request.h" #include "pair.h" #include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" -#include "timer.h" -#include "universe.h" #include "update.h" -#include "utils.h" #include -#include -#include -#include #ifdef _LMP_INTEL_OFFLOAD #ifndef INTEL_OFFLOAD_NOAFFINITY diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp index a072e823a467aa2bb9f84eeeea682695616af17f..2122bfd370998a706dcaaad733bda0de8931dfa5 100644 --- a/src/USER-INTEL/fix_nh_intel.cpp +++ b/src/USER-INTEL/fix_nh_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "fix_nh_intel.h" + #include "atom.h" -#include "compute.h" #include "domain.h" #include "error.h" #include "force.h" -#include "kspace.h" #include "memory.h" #include "modify.h" #include "neighbor.h" @@ -29,7 +28,6 @@ #include #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp index 7eeb8a163557ef9c8521bffea5090a5ff4879601..55e51227f46dc8ef0965e7d797071716eb34565d 100644 --- a/src/USER-INTEL/fix_nve_asphere_intel.cpp +++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp @@ -15,18 +15,16 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include #include "fix_nve_asphere_intel.h" -#include "math_extra_intel.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" +#include "error.h" #include "force.h" +#include "math_extra_intel.h" +#include "memory.h" #include "neighbor.h" #include "update.h" -#include "memory.h" -#include "error.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index f5a5dabfb1dc42a4ad098f5c9fc5cdca179f325e..4382542710fe850916011f09cf94c6c3e75cbd6d 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -11,18 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "fix_nvt_sllod_intel.h" -#include "math_extra.h" + #include "atom.h" +#include "compute.h" #include "domain.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "compute.h" -#include "error.h" +#include "group.h" +#include "math_extra.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 4562c63cdbe9e3c69bb793cdbb851e9c00a5b412..ba5ff79cd55e346cfd6a9875f128f8bcf208e817 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -15,22 +15,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "improper_cvff_intel.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index fc5cf08c529666e24adb587dbecf16046bb334b9..8da3c67022ab5dae52d92a92acf6cb4173c6c2f4 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -15,22 +15,23 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include + #include "improper_harmonic_intel.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "domain.h" +#include "error.h" #include "force.h" -#include "update.h" #include "math_const.h" #include "memory.h" #include "modify.h" +#include "neighbor.h" #include "suffix.h" -#include "error.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index 04791dee78eef3d4dfb6e5e6e093bbc1ca53bfbf..dc5b0fad5a633d0f9f026e3282500a7499f07fd8 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -12,8 +12,8 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "intel_buffers.h" + #include "force.h" #include "memory.h" diff --git a/src/USER-INTEL/nbin_intel.cpp b/src/USER-INTEL/nbin_intel.cpp index 78c62463896da17104f53e0dd31f84c9372cb1cc..4a046bc845e36ac8af7838dc194581a4e8b99364 100644 --- a/src/USER-INTEL/nbin_intel.cpp +++ b/src/USER-INTEL/nbin_intel.cpp @@ -16,13 +16,13 @@ ------------------------------------------------------------------------- */ #include "nbin_intel.h" + #include "atom.h" -#include "group.h" #include "comm.h" -#include "domain.h" +#include "error.h" +#include "group.h" #include "modify.h" #include "update.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 00b032d49513d512b8bc67dbcebfefb53e7fa2f3..bd4a95f77467402fe3d14bacaeb6f6dbf2b1c351 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -16,15 +16,13 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_ghost_intel.h" -#include "neighbor.h" -#include "nstencil.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" -#include "domain.h" -#include "molecule.h" #include "error.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_full_bin_intel.cpp b/src/USER-INTEL/npair_full_bin_intel.cpp index 4ef84be75ff0cffadce6e5afb54408e58c65dd98..c4433ba16cbe9bfeb85c109857f28d3e3619ab8d 100644 --- a/src/USER-INTEL/npair_full_bin_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_half_bin_newton_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_intel.cpp index 799ba2b57b67e26e88b8a9a959a23d5fbd4a8167..55bac4cdb7e94aa2276788854d93b976a76031dd 100644 --- a/src/USER-INTEL/npair_half_bin_newton_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp index 1f859cb5f1bc821202ceb80271d4e336c3772fd0..d5384904e5b4c57d67167c4b336550cdc31a8df5 100644 --- a/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp +++ b/src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_newton_tri_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" #include "comm.h" -#include "domain.h" -#include "group.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/USER-INTEL/npair_halffull_newton_intel.cpp index 8248f2257ae4f9df7c7d04ff6892071437d5d512..dd11802797c949e08ff6c7234d3261258c8642af 100644 --- a/src/USER-INTEL/npair_halffull_newton_intel.cpp +++ b/src/USER-INTEL/npair_halffull_newton_intel.cpp @@ -16,16 +16,14 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" +#include "error.h" #include "modify.h" -#include "molecule.h" -#include "domain.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index f7a233efc9791f88dad47180fd893af20068a42f..9aae0d27b788a0340359348b6a24fca136399d95 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -15,13 +15,13 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" +#include "npair_intel.h" + #include "comm.h" #include "domain.h" -#include "timer.h" #include "modify.h" -#include "npair_intel.h" -#include "nstencil.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h index 6d4e01462f5684c28daf3ccfc7a13aae056884a9..e040a1d8f3e94cc86a09b5b7404187d68b4e4a2e 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/USER-INTEL/npair_intel.h @@ -15,6 +15,7 @@ #define LMP_NPAIR_INTEL_H #include "npair.h" +#include "domain.h" #include "fix_intel.h" #if defined(_OPENMP) diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/USER-INTEL/npair_skip_intel.cpp index fa202d5da1ab604fa26c725ab14c1eae6e037b59..df09829c8600a1e62633e27197cd62d5cd838d1a 100644 --- a/src/USER-INTEL/npair_skip_intel.cpp +++ b/src/USER-INTEL/npair_skip_intel.cpp @@ -16,17 +16,15 @@ ------------------------------------------------------------------------- */ #include "npair_skip_intel.h" -#include "neighbor.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "comm.h" +#include "error.h" #include "modify.h" -#include "molecule.h" -#include "neigh_request.h" -#include "domain.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index c1e4a5374a2205e23b905479df0625a9b95b721e..6b576220fe074d5498c153e6bb67a420fc9448e1 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -15,41 +15,37 @@ Contributing author: Markus Hohnerbach (RWTH) ------------------------------------------------------------------------- */ -#ifdef __INTEL_OFFLOAD -#pragma offload_attribute(push, target(mic)) -#endif -#include -#include -#include -#include -#include -#include // requires C++-11 +#include "pair_airebo_intel.h" + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" + #include -#include -#include "lmptype.h" +#include +#include + #include "intel_preprocess.h" #include "intel_intrinsics_airebo.h" + #ifdef __INTEL_OFFLOAD #pragma offload_attribute(pop) #endif +#ifdef __INTEL_OFFLOAD +#pragma offload_attribute(push, target(mic)) +#endif + #if defined(_OPENMP) #include #endif -#include "pair_airebo_intel.h" -#include "atom.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "group.h" -#include "kspace.h" -#include "modify.h" -#include "suffix.h" -#include "math_const.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/pair_airebo_morse_intel.cpp b/src/USER-INTEL/pair_airebo_morse_intel.cpp index f68e299fa0ed22867ca586f7a876b1f49d36d430..a99ab913ba681e3abb494da12fac9299c4cc7098 100644 --- a/src/USER-INTEL/pair_airebo_morse_intel.cpp +++ b/src/USER-INTEL/pair_airebo_morse_intel.cpp @@ -16,7 +16,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse_intel.h" -#include "error.h" using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 4ad4398fbe6373ceefe935a77807d64d131234ca..a67db0ad327a8c4b35f962f7a63e66fd50552cb2 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_buck_coul_cut_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index 150cfd3ee07f9b53bc058394d849cb580df985e6..d0cb1837c90ba28adf99bbe3ba6660d9e4207a2e 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_buck_coul_long_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index b21ce13a3423b301ff38f476d0b90e8553ab1abf..bb5b44d2609ad20f17b75c73dcd3d3d358175c12 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -15,20 +15,20 @@ Contributing author: Rodrigo Canales (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include #include "pair_buck_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "group.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" +#include "error.h" #include "math_const.h" #include "memory.h" -#include "suffix.h" -#include "force.h" #include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "suffix.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp index 31430e4bf71c68215703a82ee1176487c7bc3c76..084714daf4bad388f364e20cb0e8b6f4d9789b6d 100644 --- a/src/USER-INTEL/pair_eam_alloy_intel.cpp +++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp @@ -15,18 +15,16 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_alloy_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp index c5804922f6c676b27f7b938934352682efe626e1..8786c0d782289e9000afab8fa0bb2be5d919f7b4 100644 --- a/src/USER-INTEL/pair_eam_fs_intel.cpp +++ b/src/USER-INTEL/pair_eam_fs_intel.cpp @@ -15,18 +15,16 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_fs_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 994f0d3910123f26ad03b512b44e9e2c0af245c3..561621a388e58f2d5e1842051bcf1ac1e74f6c86 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -15,22 +15,22 @@ Contributing authors: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_eam_intel.h" + #include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" #include "suffix.h" +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 1024 diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index ff8a9869b7ad606832cd0537c2fdff1f6c76b13e..c8e4a3d0efaedbce0b77e76af36d0745d83ebf2c 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -12,19 +12,22 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_charmm_coul_charmm_intel.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "group.h" #include "memory.h" #include "modify.h" #include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" #include "suffix.h" + +#include +#include + using namespace LAMMPS_NS; #define LJ_T typename IntelBuffers::vec4_t diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index 243c7f577d36f2e22ef3feadd86d4d33d0e5eedd..34ab97fd35747863368988fb58d90748714353d4 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -12,20 +12,21 @@ Contributing author: W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include #include "pair_lj_cut_coul_long_intel.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "group.h" #include "kspace.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" + +#include + using namespace LAMMPS_NS; #define C_FORCE_T typename ForceConst::c_force_t diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp index 8b9670f41917df66487a1b53dad343f96f59e9dc..533252d018d674f7b7136a78bf2c125d1e699be8 100644 --- a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp @@ -15,21 +15,16 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include #include "pair_lj_long_coul_long_intel.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "group.h" -#include "kspace.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" +#include "neighbor.h" #include "suffix.h" - using namespace LAMMPS_NS; #define C_FORCE_T typename ForceConst::c_force_t diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 32afcbf8a99a08f5ac74a1ac46218d880f4651d8..4ec2af40b00b21ac2a714b9e46c508e52f8fd568 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -17,6 +17,19 @@ #include "pair_sw_intel.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "neighbor.h" +#include "suffix.h" + +#include + #ifdef _LMP_INTEL_OFFLOAD #pragma offload_attribute(push,target(mic)) #endif @@ -25,21 +38,6 @@ #pragma offload_attribute(pop) #endif -#include -#include -#include -#include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" -#include "modify.h" -#include "suffix.h" #ifdef LMP_USE_AVXCD #include "intel_simd.h" diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index 878402932061e2a727c2f7212e0dcacd7a936dbf..75f5f85f2dcbff87f873f7e38eddb4d40857ead1 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -17,7 +17,7 @@ #include #include -#include + #include #include "pair_tersoff_intel.h" #include "atom.h" diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 270299b4c5b3267ca0705f04fef3e0cdacda4d7c..1149c9b2c35753d536b756f8e275175f75076a43 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -15,23 +15,23 @@ Contributing authors: William McDoniel (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "pppm_disp_intel.h" + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "modify.h" -#include "fft3d_wrap.h" #include "gridcomm.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "modify.h" #include "suffix.h" +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index 26af974086037ee091a3f18a99173449d1841e47..d596df44900541f20b26ebc87d2ed6001cfec960 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -18,23 +18,24 @@ W. Michael Brown (Intel) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include #include "pppm_intel.h" + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" -#include "modify.h" -#include "fft3d_wrap.h" #include "gridcomm.h" #include "math_const.h" #include "math_special.h" #include "memory.h" +#include "modify.h" #include "suffix.h" +#include +#include + +#include "omp_compat.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index 8ad3dbe33e64619fc61579eb735edad7f9e45b0e..204a9c073b5945ff4ca707b74e5d548d8fe4cbea 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -18,8 +18,8 @@ #include "fix_lb_fluid.h" #include -#include -#include + + #include #include #include diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp index 10fffed0189c833dab7e106a0bd92cfd32a392bd..0a307790d530c107e5364024e0b0c191cbf6afda 100644 --- a/src/USER-LB/fix_lb_momentum.cpp +++ b/src/USER-LB/fix_lb_momentum.cpp @@ -19,8 +19,8 @@ ------------------------------------------------------------------------- */ #include "fix_lb_momentum.h" -#include -#include + + #include #include "atom.h" #include "group.h" diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp index d61692419a1bd3ef51512c661d2783adb13a04af..2c7e8dbf4768a5f5cee3f486b2376f63bfc524a7 100644 --- a/src/USER-LB/fix_lb_pc.cpp +++ b/src/USER-LB/fix_lb_pc.cpp @@ -26,7 +26,7 @@ #include "domain.h" #include "fix_lb_fluid.h" #include "modify.h" -#include + #include "group.h" using namespace LAMMPS_NS; diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 9cc03591fa6373d516b19e61c0452f10f4664bfd..f714e317193dad2f3eba654a859003e712121e26 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -17,9 +17,9 @@ ------------------------------------------------------------------------- */ #include "fix_lb_rigid_pc_sphere.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" @@ -31,7 +31,7 @@ #include "memory.h" #include "error.h" #include "fix_lb_fluid.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 41074903bdd9eb53d04e09bdd99bac25d4104bd4..732ba0909e3d58fc024831c26e2569e9b12d5184 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "fix_manifoldforce.h" // For stuff -#include -#include -#include "atom.h" -#include "update.h" -#include "respa.h" -#include "error.h" -#include "force.h" #include "manifold.h" #include "manifold_factory.h" // For constructing manifold +#include "atom.h" +#include "error.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 2baa2944aef77b34ffd8561b80ddb7803b8d6e87..b3122a68d4036d380b1833ee0ba11cc5d8a03dd1 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -33,7 +33,7 @@ #include "fix_nve_manifold_rattle.h" -#include + #include #include "atom.h" #include "force.h" diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp index b9b7ae7279851f09ab37c705f49bbf1b0298e4cc..ef269992950e8ea49fbc34a66b05621c4eb8f0da 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp @@ -3,6 +3,8 @@ #include "comm.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace user_manifold; diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h index b4f8fd341ba931e321350c38ad8e8c2614362946..b974ce5bc834e249f34092dd61c280f33dc38258 100644 --- a/src/USER-MEAMC/meam.h +++ b/src/USER-MEAMC/meam.h @@ -1,9 +1,23 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #ifndef LMP_MEAM_H #define LMP_MEAM_H +#include "math_const.h" // IWYU pragma: export + #include #include -#include "math_const.h" #define maxelt 5 diff --git a/src/USER-MEAMC/meam_dens_final.cpp b/src/USER-MEAMC/meam_dens_final.cpp index fe9e74ca7cf6690ab3050b8249f4a8b1bb45a6f3..02c461e6b760581e4316304dc6f30a5e956955c1 100644 --- a/src/USER-MEAMC/meam_dens_final.cpp +++ b/src/USER-MEAMC/meam_dens_final.cpp @@ -1,3 +1,15 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_dens_init.cpp b/src/USER-MEAMC/meam_dens_init.cpp index 39e3ff94679710438ca5426ece1b73f6ca43c50f..7a5ee7a6518aebb5bf08a6e9976dc59287f8a32c 100644 --- a/src/USER-MEAMC/meam_dens_init.cpp +++ b/src/USER-MEAMC/meam_dens_init.cpp @@ -1,7 +1,21 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" -#include -#include "memory.h" + #include "math_special.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_force.cpp b/src/USER-MEAMC/meam_force.cpp index 2b6832e155a34fdd57ea5015cea6424541aeab5c..eba4f79ea914c48ce3a2b3309c6a83f6c2f2d885 100644 --- a/src/USER-MEAMC/meam_force.cpp +++ b/src/USER-MEAMC/meam_force.cpp @@ -1,11 +1,24 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" + +#include "math_special.h" + #include #include -#include "math_special.h" using namespace LAMMPS_NS; - void MEAM::meam_force(int i, int eflag_either, int eflag_global, int eflag_atom, int vflag_atom, double* eng_vdwl, double* eatom, int /*ntype*/, int* type, int* fmap, double** scale, double** x, int numneigh, int* firstneigh, diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 706075ffd0183c9902a7c0d1b3ebd2f35befff6b..0a632bc40afbf57ea4c90cd54d98e5ea1c23fdb3 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -16,7 +16,9 @@ ------------------------------------------------------------------------- */ #include "meam.h" + #include "math_special.h" + #include using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index 0a0b95e14a05c735c6637dd4bc6436c308961928..a546aa0c7f1498c5cae0379cf0c667342939b544 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -16,9 +16,11 @@ ------------------------------------------------------------------------- */ #include "meam.h" -#include + #include "memory.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index 25f1bb9e81d93e6159138511f752684e1db28bfe..ddbb40310c7af08bb39c12e61f647f23f8184e4e 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -1,9 +1,23 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" + +#include "math_special.h" +#include "memory.h" + #include #include #include -#include "math_special.h" -#include "memory.h" using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp index 60264b87cb2c82b14cc9f229206b82a2d3f9f5ee..93b866a14f5189e63f6fe026e79825d99898a24b 100644 --- a/src/USER-MEAMC/meam_setup_global.cpp +++ b/src/USER-MEAMC/meam_setup_global.cpp @@ -1,5 +1,19 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ #include "meam.h" + #include + using namespace LAMMPS_NS; template diff --git a/src/USER-MEAMC/meam_setup_param.cpp b/src/USER-MEAMC/meam_setup_param.cpp index f0e04ff1c091f855e6f503662e793cfc467c1c52..f2c44504dee48aaff07d18af888d2bf5d4f1cd27 100644 --- a/src/USER-MEAMC/meam_setup_param.cpp +++ b/src/USER-MEAMC/meam_setup_param.cpp @@ -1,5 +1,22 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + #include "meam.h" + +#include "math_const.h" #include +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index f40df56c19b6458bdb100d7785c9717d973bdb0a..6f674c9f4526c458a80b76bcbec6b94fae41a26d 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "pair_meamc.h" -#include -#include + + #include -#include + #include "meam.h" #include "atom.h" #include "force.h" @@ -29,8 +29,8 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index 21e44e7ff2538fbe2fa26f85f2a76e789523975d..9cbda8f6ad07b8e42d6bc0b5607e8a774f8c696d 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -22,7 +22,7 @@ PairStyle(meam,PairMEAMC) #define LMP_PAIR_MEAMC_H #include "pair.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MESODPD/atom_vec_edpd.cpp b/src/USER-MESODPD/atom_vec_edpd.cpp index d08a626fad6e6ccf3e62e3661b9e0bc668e0669b..1542c73604aab773caed196faf33a877b1a08c3a 100644 --- a/src/USER-MESODPD/atom_vec_edpd.cpp +++ b/src/USER-MESODPD/atom_vec_edpd.cpp @@ -12,16 +12,13 @@ ------------------------------------------------------------------------- */ #include "atom_vec_edpd.h" -#include + #include "atom.h" -#include "comm.h" -#include "domain.h" +#include "error.h" #include "modify.h" -#include "fix.h" #include "update.h" -#include "memory.h" -#include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/atom_vec_tdpd.cpp b/src/USER-MESODPD/atom_vec_tdpd.cpp index f50fe168d6e0dc8548d669dfcd5b1825c70e7163..63b88f921d6134291ba6a43ef69419e9aa37177e 100644 --- a/src/USER-MESODPD/atom_vec_tdpd.cpp +++ b/src/USER-MESODPD/atom_vec_tdpd.cpp @@ -16,7 +16,7 @@ #include "atom.h" #include "update.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp index bc02c93e1ad866cd0b7deaf2a0d9ba0b7f326b4a..7e9d5eb29e6cdf0a1625b6b5a40cd969705f1fc5 100644 --- a/src/USER-MESODPD/compute_tdpd_cc_atom.cpp +++ b/src/USER-MESODPD/compute_tdpd_cc_atom.cpp @@ -11,15 +11,16 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include #include "compute_tdpd_cc_atom.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/fix_edpd_source.cpp b/src/USER-MESODPD/fix_edpd_source.cpp index 9d31e5f410c3d4db75cc5a219fc581aa1c30caf3..c84f2f29a23b24cc1234067966f54b2fa07e17da 100644 --- a/src/USER-MESODPD/fix_edpd_source.cpp +++ b/src/USER-MESODPD/fix_edpd_source.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_edpd_source.h" -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MESODPD/fix_tdpd_source.cpp b/src/USER-MESODPD/fix_tdpd_source.cpp index 7c19d78b1fffe1a7ddc9c735a215b4a23a423d72..440c5055fb7fab94d29ea281b06d10f4e2b5e50b 100644 --- a/src/USER-MESODPD/fix_tdpd_source.cpp +++ b/src/USER-MESODPD/fix_tdpd_source.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_tdpd_source.h" -#include -#include + #include "atom.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MESODPD/pair_edpd.cpp b/src/USER-MESODPD/pair_edpd.cpp index 60a437a47c2f4a3f8c8e91589cff234fac186d0b..9c2e74b8823cdd555f84e441f17e4e0e538e1442 100644 --- a/src/USER-MESODPD/pair_edpd.cpp +++ b/src/USER-MESODPD/pair_edpd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_edpd.h" -#include + #include #include #include @@ -31,7 +31,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_mdpd.cpp b/src/USER-MESODPD/pair_mdpd.cpp index 755008f44310e075f7eebd1085c00c430fab0ced..88b6724a03a2c60adae5284f9b56f3bd5bf42032 100644 --- a/src/USER-MESODPD/pair_mdpd.cpp +++ b/src/USER-MESODPD/pair_mdpd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_mdpd.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_mdpd_rhosum.cpp b/src/USER-MESODPD/pair_mdpd_rhosum.cpp index bfbc6f7c82493e1dc33f61896644d5431aa91fea..2f25177b0a31579c75013b00de80d613797e0403 100644 --- a/src/USER-MESODPD/pair_mdpd_rhosum.cpp +++ b/src/USER-MESODPD/pair_mdpd_rhosum.cpp @@ -20,16 +20,16 @@ ------------------------------------------------------------------------- */ #include "pair_mdpd_rhosum.h" -#include + #include "atom.h" -#include "force.h" #include "comm.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "neighbor.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MESODPD/pair_tdpd.cpp b/src/USER-MESODPD/pair_tdpd.cpp index face9221d969ff9dce09d9949e0be7f5cfb08424..65a518c07e525e6675952a708f46de520eac2b26 100644 --- a/src/USER-MESODPD/pair_tdpd.cpp +++ b/src/USER-MESODPD/pair_tdpd.cpp @@ -29,7 +29,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MESONT/compute_mesont.cpp b/src/USER-MESONT/compute_mesont.cpp index 397b071a1be4a1a718c493766d383102dde3c88e..96792c8988710fe1c2dbfb9752fbc9470ad87194 100644 --- a/src/USER-MESONT/compute_mesont.cpp +++ b/src/USER-MESONT/compute_mesont.cpp @@ -23,7 +23,7 @@ #include "memory.h" #include "error.h" #include "pair.h" -#include + using namespace LAMMPS_NS; diff --git a/src/USER-MESONT/pair_mesocnt.cpp b/src/USER-MESONT/pair_mesocnt.cpp index 4af8a99d6f6b66ff89901aada7ad9bdeebba7793..96d53bd41a641890c932b5c6ff96b55965f0275a 100644 --- a/src/USER-MESONT/pair_mesocnt.cpp +++ b/src/USER-MESONT/pair_mesocnt.cpp @@ -20,9 +20,9 @@ #include #include -#include + #include -#include + #include "atom.h" #include "comm.h" @@ -33,8 +33,8 @@ #include "memory.h" #include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-MESONT/pair_mesont_tpm.cpp b/src/USER-MESONT/pair_mesont_tpm.cpp index 9fb0f604c82cee8047a754cae8bae33111fe1bc2..6d8c8126ae29f8e53859e34cfcdee3850bfb96e9 100644 --- a/src/USER-MESONT/pair_mesont_tpm.cpp +++ b/src/USER-MESONT/pair_mesont_tpm.cpp @@ -16,7 +16,7 @@ #include "pair_mesont_tpm.h" #include "export_mesont.h" -#include + #include "atom.h" #include "comm.h" #include "force.h" @@ -29,7 +29,7 @@ #include #include #include -#include + #include #include #include diff --git a/src/USER-MGPT/pair_mgpt.cpp b/src/USER-MGPT/pair_mgpt.cpp index e7ab62608ada9165225e9efdae12a816653d69ac..070e3cb61e24c3dce8ab266505518a97b1632a63 100644 --- a/src/USER-MGPT/pair_mgpt.cpp +++ b/src/USER-MGPT/pair_mgpt.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "pair_mgpt.h" -#include + #include -#include + #include #include diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index 2ed1a8567282dede28b15475f058d2318024e922..a986cb83220d4042f3ea4ad2597dae2b17ce5d3f 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index fb1cc0a4e6887612627f57e3cd266765dfe773f4..52bfe751f14a77c008014e68a4294a443816f1d3 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_shift_exp.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index 6e449fe4720e069de1687ad35efa0ef7771ef89c..336638f25d6c0ccae74a84e75805e5dfa94ca0cf 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_dipole.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index 5f34be8d65ebc535396b232ff905abee6d17d457..907ee973bde9f5d7fec4a7377e6457a04d51b535 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_fourier.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index cddc07da9028c24aaf3ce2745f8be4def288be3e..8894f7b4c9199cb0dec9d1929827ef6bc98aba6e 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_fourier_simple.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index c84739ac914082e5a3a774ee127354b10c36ed80..93f45f9562b2cd0ba293344d8520c4233423bd8d 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_quartic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index dd2c1a1524d9455097d2a03aac466148d0c92b42..5889400b978fdf0b4ab9c4cea08ac8583a748ad4 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_shift.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index 2cbfa01c0ad68bf8c04679b88a355003b64744f6..86e6263f93374ad1f9a6d64d2d480ef741c989b5 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_harmonic_shift_cut.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_special.cpp b/src/USER-MISC/bond_special.cpp index ebbdcb1899344ecc1cfea664c85426e03c6b51fe..87671655b1980d8506eb2a0c09f009c63fd2ebe1 100644 --- a/src/USER-MISC/bond_special.cpp +++ b/src/USER-MISC/bond_special.cpp @@ -13,19 +13,15 @@ Contributing Author: David Nicholson (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "bond_special.h" + #include "atom.h" -#include "neighbor.h" -#include "domain.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" +#include "pair.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/bond_special.h b/src/USER-MISC/bond_special.h index 389990b1d7969671fb808c9eeee35e6a196e1681..d5e360ca537920abe5866f5556be42abf53fccb0 100644 --- a/src/USER-MISC/bond_special.h +++ b/src/USER-MISC/bond_special.h @@ -22,7 +22,6 @@ BondStyle(special,BondSpecial) #ifndef LMP_BOND_SPECIAL_H #define LMP_BOND_SPECIAL_H -#include #include "bond.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp index fdce944034a064b228001e98b3fbb58112de35bc..52656ec9d68138efdb04c4e73a7dba6b11cdea30 100644 --- a/src/USER-MISC/compute_cnp_atom.cpp +++ b/src/USER-MISC/compute_cnp_atom.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "compute_cnp_atom.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/compute_hma.cpp b/src/USER-MISC/compute_hma.cpp index ccecf43aaf4ad1bef997daba65dc2e7588122f0a..f2ccf2694de3db2d14353164393a67b180dfa792 100644 --- a/src/USER-MISC/compute_hma.cpp +++ b/src/USER-MISC/compute_hma.cpp @@ -43,33 +43,30 @@ properties of crystals by molecular simulation”, Phys. Rev. E 92, 043303 (2015 https://doi.org/10.1103/PhysRevE.92.043303 ------------------------------------------------------------------------- */ -#include -#include -#include #include "compute_hma.h" + +#include "angle.h" #include "atom.h" -#include "update.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" -#include "improper.h" -#include "kspace.h" -#include "group.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_store.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "kspace.h" #include "memory.h" -#include "error.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_request.h" +#include "modify.h" #include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" -#include - +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/compute_momentum.cpp b/src/USER-MISC/compute_momentum.cpp index 541b52d9c04014ca81771d61caeaa7df4de69d8e..f1c35993e378431a7a4164ea3abcfca9a2fd0c67 100644 --- a/src/USER-MISC/compute_momentum.cpp +++ b/src/USER-MISC/compute_momentum.cpp @@ -1,6 +1,6 @@ #include "compute_momentum.h" -#include + #include "atom.h" #include "error.h" #include "update.h" diff --git a/src/USER-MISC/compute_pressure_cylinder.cpp b/src/USER-MISC/compute_pressure_cylinder.cpp index 8346bd3410101904d08001991ae52b0783b4541f..6cf375dd19d4f512b6dadc478cc75db40e89ea08 100644 --- a/src/USER-MISC/compute_pressure_cylinder.cpp +++ b/src/USER-MISC/compute_pressure_cylinder.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pressure_cylinder.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index 1e42a9df029720922184afc8fdf01e91f8c3e03f..c733c929ba4583244656f4a836475c2d012cd05c 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -16,7 +16,7 @@ --------------------------------------------------------------------------*/ #include "compute_stress_mop.h" -#include + #include #include diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 022840166f6d5fe33d5ded2fc525eb67643a8440..323aee851ee50bc96eb67dc1b378a332784ff000 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -16,7 +16,7 @@ --------------------------------------------------------------------------*/ #include "compute_stress_mop_profile.h" -#include + #include #include diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp index 94c6115186176b84ba035b874327e5990611ef02..c333357a93df328eba2b60415047fc7f4a42b44d 100644 --- a/src/USER-MISC/compute_temp_rotate.cpp +++ b/src/USER-MISC/compute_temp_rotate.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_rotate.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/USER-MISC/compute_viscosity_cos.cpp b/src/USER-MISC/compute_viscosity_cos.cpp index 7311f991ccdbfe737ba1e19424e2d73e4a520fb5..dae93a8d81a02bf35e39edb1be3d07218d047357 100644 --- a/src/USER-MISC/compute_viscosity_cos.cpp +++ b/src/USER-MISC/compute_viscosity_cos.cpp @@ -15,17 +15,18 @@ Contributing author: Zheng GONG (ENS de Lyon, z.gong@outlook.com) ------------------------------------------------------------------------- */ -#include #include "compute_viscosity_cos.h" + #include "atom.h" #include "update.h" #include "force.h" #include "domain.h" -#include "comm.h" #include "group.h" #include "error.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 1b3afb13eb07473f50fc1176382a9394bfb6ae4f..7c131682fa567ed4b000f25341b00f3477ea9949 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_cosine_shift_exp.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index e897e58649c2f432d2533b5431f1f907025f2c4d..066447f92d91ccb4e4e4e7b6fe8868bb577acf45 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_fourier.h" -#include + #include #include "atom.h" #include "comm.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index 0ff62320e4c534a82671572098d98f3c60a3fc69..bde8d84070bd68486a11603991f647ef25db94fc 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_nharmonic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index d91c237838acaa37ed67993ca7c8637c8643fab9..deafc8391f671dc577cb1b19a00af4b850d519fe 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_quadratic.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -27,7 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 1cfb7561278ad80fc3c6fb12211c488396b0e753..15bb458c481631d5cef0bacb55e9ed78d685c444 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -18,21 +18,20 @@ ------------------------------------------------------------------------- */ #include "dihedral_spherical.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "error.h" #include "force.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" + +#include +#include -using namespace std; using namespace LAMMPS_NS; using namespace MathConst; using namespace MathExtra; diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index 37410ba085ea9d9e5e48a05ee87f936346b3d5d3..91a8642b10ec4480d8a91b19d665e33be32e9efb 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -17,33 +17,24 @@ the "tridiag.c" written by Gerard Jungman for GSL ------------------------------------------------------------------------- */ -#include -#include -#include -#include -#include -#include -#include // IWYU pragma: keep -#include // IWYU pragma: keep +#include "dihedral_table.h" #include "atom.h" #include "comm.h" -#include "neighbor.h" #include "domain.h" +#include "error.h" #include "force.h" +#include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "dihedral_table.h" -#include "utils.h" -#include "tokenizer.h" +#include "neighbor.h" #include "table_file_reader.h" -#include "fmt/format.h" +#include "tokenizer.h" -#include "math_const.h" -#include "math_extra.h" +#include +#include +#include // IWYU pragma: keep -using namespace std; using namespace LAMMPS_NS; using namespace MathConst; using namespace MathExtra; @@ -829,28 +820,20 @@ void DihedralTable::coeff(int narg, char **arg) // --- and resolve issues with periodicity --- if (tb->ninput < 2) { - string err_msg; - err_msg = string("Invalid dihedral table length (") - + string(arg[2]) + string(")."); - error->one(FLERR,err_msg); - } - else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { - string err_msg; - err_msg = string("Invalid dihedral spline table length. (Try linear)\n (") - + string(arg[2]) + string(")."); - error->one(FLERR,err_msg); + error->one(FLERR,fmt::format("Invalid dihedral table length ({}).", + arg[2])); + } else if ((tb->ninput == 2) && (tabstyle == SPLINE)) { + error->one(FLERR,fmt::format("Invalid dihedral spline table length. " + "(Try linear)\n ({}).",arg[2])); } // check for monotonicity for (int i=0; i < tb->ninput-1; i++) { if (tb->phifile[i] >= tb->phifile[i+1]) { - stringstream i_str; - i_str << i+1; - string err_msg = - string("Dihedral table values are not increasing (") + - string(arg[2]) + string(", ")+i_str.str()+string("th entry)"); + auto err_msg = fmt::format("Dihedral table values are not increasing " + "({}, {}th entry)",arg[2],i+1); if (i==0) - err_msg += string("\n(This is probably a mistake with your table format.)\n"); + err_msg += std::string("\n(This is probably a mistake with your table format.)\n"); error->all(FLERR,err_msg); } } @@ -859,20 +842,13 @@ void DihedralTable::coeff(int narg, char **arg) double philo = tb->phifile[0]; double phihi = tb->phifile[tb->ninput-1]; if (tb->use_degrees) { - if ((phihi - philo) >= 360) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 360 degrees (") - +string(arg[2]) + string(")."); - error->all(FLERR,err_msg); - } - } - else { - if ((phihi - philo) >= MY_2PI) { - string err_msg; - err_msg = string("Dihedral table angle range must be < 2*PI radians (") - + string(arg[2]) + string(")."); - error->all(FLERR,err_msg); - } + if ((phihi - philo) >= 360) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 360 " + "degrees ({}).",arg[2])); + } else { + if ((phihi - philo) >= MY_2PI) + error->all(FLERR,fmt::format("Dihedral table angle range must be < 2*PI " + "radians ({}).",arg[2])); } // convert phi from degrees to radians @@ -940,10 +916,9 @@ void DihedralTable::coeff(int narg, char **arg) // Optional: allow the user to print out the interpolated spline tables if (me == 0) { - if (!checkU_fname.empty()) - { - ofstream checkU_file; - checkU_file.open(checkU_fname, ios::out); + if (!checkU_fname.empty()) { + std::ofstream checkU_file; + checkU_file.open(checkU_fname, std::ios::out); for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double u = tb->e[i]; @@ -953,12 +928,10 @@ void DihedralTable::coeff(int narg, char **arg) } checkU_file.close(); } - if (!checkF_fname.empty()) - { - ofstream checkF_file; - checkF_file.open(checkF_fname, ios::out); - for (int i=0; i < tablength; i++) - { + if (!checkF_fname.empty()) { + std::ofstream checkF_file; + checkF_file.open(checkF_fname, std::ios::out); + for (int i=0; i < tablength; i++) { double phi = i*MY_2PI/tablength; double f; if ((tabstyle == SPLINE) && (tb->f_unspecified)) { @@ -973,8 +946,7 @@ void DihedralTable::coeff(int narg, char **arg) // To be nice and report something, I do the same thing here.) cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi); f = -dU_dphi; - } - else + } else // Otherwise we calculated the tb->f[] array. Report its contents. f = tb->f[i]; if (tb->use_degrees) { @@ -991,8 +963,7 @@ void DihedralTable::coeff(int narg, char **arg) // store ptr to table in tabindex int count = 0; - for (int i = ilo; i <= ihi; i++) - { + for (int i = ilo; i <= ihi; i++) { tabindex[i] = ntables; //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported setflag[i] = 1; @@ -1213,7 +1184,7 @@ void DihedralTable::spline_table(Table *tb) } // for (int i=0; ininput; i++) if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) { - string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); + std::string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n"); error->all(FLERR, msg); } @@ -1319,7 +1290,7 @@ void DihedralTable::param_extract(Table *tb, char *line) ValueTokenizer values(line); while (values.has_next()) { - std::string word = values.next_string(); + auto word = values.next_string(); if (word == "N") { tb->ninput = values.next_int(); } @@ -1342,10 +1313,8 @@ void DihedralTable::param_extract(Table *tb, char *line) //else if (word == "EQ") { // tb->theta0 = values.next_double(); //} - else { - string err_msg = fmt::format("Invalid keyword in dihedral angle table parameters ({})", word); - error->one(FLERR,err_msg); - } + else error->one(FLERR,fmt::format("Invalid keyword in dihedral angle " + "table parameters ({})", word)); } } catch (TokenizerException & e) { error->one(FLERR, e.what()); diff --git a/src/USER-MISC/dihedral_table.h b/src/USER-MISC/dihedral_table.h index 8a397b20f2daba55d7908085f816b5fc3eb7c742..a8d1f8f8bbfe2ee8eb718375c904337258495971 100644 --- a/src/USER-MISC/dihedral_table.h +++ b/src/USER-MISC/dihedral_table.h @@ -24,7 +24,7 @@ DihedralStyle(table,DihedralTable) #ifndef LMP_DIHEDRAL_TABLE_H #define LMP_DIHEDRAL_TABLE_H #include "dihedral.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 2a5b46a4f1608536fbd3d625345684a35507372e..f8a2f025966a8e1e02ae46e7f21406e140350f39 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -17,12 +17,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_table_cut.h" -#include + #include #include -#include + #include -#include + #include // IWYU pragma: keep #include // IWYU pragma: keep @@ -35,7 +35,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/fix_accelerate_cos.cpp b/src/USER-MISC/fix_accelerate_cos.cpp index 17d6e9ad9470f88af7d44a1b73682ba604cef165..4c156855569db8e23f22b4624dbc2b7481c9dfa7 100644 --- a/src/USER-MISC/fix_accelerate_cos.cpp +++ b/src/USER-MISC/fix_accelerate_cos.cpp @@ -16,19 +16,15 @@ ------------------------------------------------------------------------- */ #include "fix_accelerate_cos.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "region.h" -#include "respa.h" -#include "input.h" -#include "variable.h" -#include "memory.h" #include "error.h" #include "force.h" #include "math_const.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp index 4583d76e0969878ead45e3eb2e6a8239646d3b6a..ed796280e79ea006841d2a0125343b78cd3fe035 100644 --- a/src/USER-MISC/fix_addtorque.cpp +++ b/src/USER-MISC/fix_addtorque.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_addtorque.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index abfa751d158c5dd6f6e697f9b087d9949e3c3993..d92789f03fa2c6a7214f9501ed6f55a1b521dd48 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -22,20 +22,19 @@ ------------------------------------------------------------------------- */ #include "fix_ave_correlate_long.h" -#include -#include -#include -#include -#include -#include "update.h" -#include "modify.h" + +#include "citeme.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" -#include "citeme.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_electron_stopping.cpp b/src/USER-MISC/fix_electron_stopping.cpp index bf970662758eb0fc8f6d8265c22cb0b48d5d42c6..952ffe758418d0e9caac84b6f2ca8b1b2f914598 100644 --- a/src/USER-MISC/fix_electron_stopping.cpp +++ b/src/USER-MISC/fix_electron_stopping.cpp @@ -17,21 +17,22 @@ ------------------------------------------------------------------------- */ #include "fix_electron_stopping.h" -#include -#include -#include "mpi.h" + #include "atom.h" -#include "update.h" +#include "comm.h" #include "domain.h" -#include "region.h" -#include "force.h" +#include "error.h" #include "fix.h" +#include "force.h" #include "memory.h" -#include "comm.h" -#include "error.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" +#include "region.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index 4460c551836bc0465faaad4a44334b3742ca0cc9..fb111c1f2724a587c61acdabedbd1226a602f9e8 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -22,7 +22,7 @@ ------------------------------------------------------------------------- */ #include "fix_ffl.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 18fd7848619922979746597e27e9840942ed4b5d..86650cd50d7f8b6de8cdadb8e78896ab2e49fbdc 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_filter_corotate.h" -#include + #include #include #include -#include + #include "atom.h" #include "atom_vec.h" #include "comm.h" diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp index 2463e18b400835e79dc75e25e046ef7a8b3ccfa6..d603e376714b2c8522696c3184dc27bee96bbadf 100644 --- a/src/USER-MISC/fix_flow_gauss.cpp +++ b/src/USER-MISC/fix_flow_gauss.cpp @@ -17,16 +17,16 @@ ------------------------------------------------------------------------- */ #include "fix_flow_gauss.h" -#include -#include + #include "atom.h" -#include "force.h" -#include "group.h" -#include "update.h" +#include "citeme.h" #include "domain.h" #include "error.h" -#include "citeme.h" +#include "group.h" #include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp index 30e62c7eb9051919b0d63bd3967c9e5a47ab3e30..f4776c3d6c0a4bd2fc586d70e2f3b963d1e4fb5f 100644 --- a/src/USER-MISC/fix_gle.cpp +++ b/src/USER-MISC/fix_gle.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_gle.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -29,7 +29,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp index af4a5172692e02f5a38022b984303b140dc34dd2..7c3fac9c339dc0ae3a88e57e43bc84ddb31bf106 100644 --- a/src/USER-MISC/fix_imd.cpp +++ b/src/USER-MISC/fix_imd.cpp @@ -48,17 +48,16 @@ negotiate an appropriate license for such distribution." ------------------------------------------------------------------------- */ #include "fix_imd.h" + #include "atom.h" #include "comm.h" -#include "update.h" -#include "respa.h" #include "domain.h" -#include "force.h" #include "error.h" #include "group.h" #include "memory.h" +#include "respa.h" +#include "update.h" -#include #include #if defined(_MSC_VER) || defined(__MINGW32__) diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp index b1d07eef4102fdd76259cafe3e50b812ec54b2ec..b8045a9ff1412a902f22df17503c8afebf12e30a 100644 --- a/src/USER-MISC/fix_ipi.cpp +++ b/src/USER-MISC/fix_ipi.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_ipi.h" -#include + #include #include "atom.h" #include "force.h" @@ -45,7 +45,7 @@ using namespace FixConst; // socket interface #ifndef _WIN32 -#include + #include #include #include diff --git a/src/USER-MISC/fix_momentum_chunk.cpp b/src/USER-MISC/fix_momentum_chunk.cpp index 0ed5e1f8770a56d533ca2397cdb91d3318e03e2d..fcd6d47922b1c75e65bd69769fe1064f383dbad6 100644 --- a/src/USER-MISC/fix_momentum_chunk.cpp +++ b/src/USER-MISC/fix_momentum_chunk.cpp @@ -12,19 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_momentum_chunk.h" -#include -#include -#include + #include "atom.h" #include "compute.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" #include "domain.h" -#include "group.h" #include "error.h" -#include "force.h" +#include "group.h" #include "modify.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_momentum_chunk.h b/src/USER-MISC/fix_momentum_chunk.h index 5e056f2494991b6c83dc323f135be7087c4e51f4..5007e38c695ecce03ce1bf182ba0dd46034a9b5d 100644 --- a/src/USER-MISC/fix_momentum_chunk.h +++ b/src/USER-MISC/fix_momentum_chunk.h @@ -21,7 +21,7 @@ FixStyle(momentum/chunk,FixMomentumChunk) #define LMP_FIX_MOMENTUM_CHUNK_H #include "fix.h" -#include + namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_npt_cauchy.cpp b/src/USER-MISC/fix_npt_cauchy.cpp index 221886d38871f28fb458aeca5fb691a22edd5539..9361d9ebd6f2b58a5ab91383f49f26de925442a8 100644 --- a/src/USER-MISC/fix_npt_cauchy.cpp +++ b/src/USER-MISC/fix_npt_cauchy.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "fix_npt_cauchy.h" #include "math_extra.h" diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp index 410a269f8cec30eed5258111cbc2c16ddd4e1871..f0fbddf18de46dc1ad145122783f61ff81385881 100644 --- a/src/USER-MISC/fix_nvk.cpp +++ b/src/USER-MISC/fix_nvk.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_nvk.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-MISC/fix_orient_eco.cpp b/src/USER-MISC/fix_orient_eco.cpp index 4e97cac3f94b0e554ef5e52d9c63e02de1916f50..5f1582d580c516e0b72db9ece8b161b5ee82e75d 100644 --- a/src/USER-MISC/fix_orient_eco.cpp +++ b/src/USER-MISC/fix_orient_eco.cpp @@ -16,13 +16,10 @@ ------------------------------------------------------------------------- */ #include "fix_orient_eco.h" -#include -#include -#include + #include "atom.h" #include "citeme.h" #include "comm.h" -#include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" @@ -33,8 +30,9 @@ #include "pair.h" #include "respa.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_pafi.cpp b/src/USER-MISC/fix_pafi.cpp index 33407aec44cd09bf66fe9c8e824bfa59b873d868..1ac0ffb188c8d5b7222164e58616eb5c9316655a 100644 --- a/src/USER-MISC/fix_pafi.cpp +++ b/src/USER-MISC/fix_pafi.cpp @@ -19,25 +19,22 @@ #include "fix_pafi.h" -#include -#include -#include -#include -#include "math_extra.h" + #include "atom.h" -#include "force.h" -#include "update.h" -#include "modify.h" -#include "domain.h" -#include "respa.h" +#include "citeme.h" #include "comm.h" #include "compute.h" -#include "random_mars.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "citeme.h" -#include "fmt/format.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -61,7 +58,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), random(NULL), computename(NULL), + Fix(lmp, narg, arg), computename(NULL), random(NULL), h(NULL), step_respa(NULL) { if (lmp->citeme) lmp->citeme->add(cite_fix_pafi_package); @@ -122,15 +119,15 @@ FixPAFI::FixPAFI(LAMMPS *lmp, int narg, char **arg) : } force_flag = 0; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i=0; i<6; i++) { + for (int i=0; i<6; i++) { proj[i] = 0.0; proj_all[i] = 0.0; } - for(int i=0; i<5; i++) { + for (int i=0; i<5; i++) { results[i] = 0.0; results_all[i] = 0.0; } @@ -208,14 +205,14 @@ void FixPAFI::setup(int vflag) void FixPAFI::min_setup(int vflag) { - if( utils::strmatch(update->minimize_style,"^fire")==0 && + if (utils::strmatch(update->minimize_style,"^fire")==0 && utils::strmatch(update->minimize_style,"^quickmin")==0 ) error->all(FLERR,"fix pafi requires a damped dynamics minimizer"); min_post_force(vflag); } -void FixPAFI::post_force(int vflag) +void FixPAFI::post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; @@ -236,24 +233,20 @@ void FixPAFI::post_force(int vflag) PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - double xum=0.; - // proj 0,1,2 = f.n, v.n, h.n // proj 3,4,5 = psi, f.n**2, f*(1-psi) // c_v 0,1,2 = fxcom, fycom, fzcom etc - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } double deviation[3] = {0.,0.,0.}; - double fn; - force_flag=0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -293,7 +286,7 @@ void FixPAFI::post_force(int vflag) } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -345,7 +338,7 @@ void FixPAFI::post_force(int vflag) if (od_flag == 0) { for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit) { - if(rmass) mass_f = sqrt(rmass[i]); + if (rmass) mass_f = sqrt(rmass[i]); else mass_f = sqrt(mass[type[i]]); f[i][0] += -gamma * mass_f * mass_f * v[i][0]; @@ -361,7 +354,7 @@ void FixPAFI::post_force(int vflag) for (int i = 0; i < nlocal; i++){ if (mask[i] & groupbit) { - if(rmass) mass_f = sqrt(rmass[i]); + if (rmass) mass_f = sqrt(rmass[i]); else mass_f = sqrt(mass[type[i]]); f[i][0] += sqrtD * h[i][0] * mass_f; @@ -378,13 +371,12 @@ void FixPAFI::post_force(int vflag) }; -void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) +void FixPAFI::post_force_respa(int vflag, int ilevel, int /*iloop*/) { // set force to desired value on requested level, 0.0 on other levels if (ilevel == ilevel_respa) post_force(vflag); else { - double **x = atom->x; double **f = atom->f; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -396,38 +388,31 @@ void FixPAFI::post_force_respa(int vflag, int ilevel, int iloop) } }; -void FixPAFI::min_post_force(int vflag) +void FixPAFI::min_post_force(int /*vflag*/) { double **x = atom->x; double **v = atom->v; double **f = atom->f; - double *rmass = atom->rmass; - double *mass = atom->mass; - int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - double xum=0.; - // proj 0,1,2 = f.n, v.n, h.n // proj 3,4,5 = psi, f.n**2, f*(1-psi) // c_v 0,1,2 = fxcom, fycom, fzcom etc - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } double deviation[3] = {0.,0.,0.}; - double fn; - force_flag=0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { @@ -464,7 +449,7 @@ void FixPAFI::min_post_force(int vflag) } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -519,7 +504,7 @@ double FixPAFI::compute_vector(int n) -void FixPAFI::initial_integrate(int vflag) +void FixPAFI::initial_integrate(int /*vflag*/) { double dtfm; @@ -539,11 +524,11 @@ void FixPAFI::initial_integrate(int vflag) PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } @@ -559,7 +544,7 @@ void FixPAFI::initial_integrate(int vflag) proj[1] += v[i][2] * path[i][5]; // v.n } } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -651,11 +636,11 @@ void FixPAFI::final_integrate() PathCompute->compute_peratom(); double **path = PathCompute->array_atom; - for(int i = 0; i < 10; i++) { + for (int i = 0; i < 10; i++) { c_v[i] = 0.; c_v_all[i] = 0.; } - for(int i = 0; i < 6; i++) { + for (int i = 0; i < 6; i++) { proj[i] = 0.; proj_all[i] = 0.; } @@ -665,7 +650,7 @@ void FixPAFI::final_integrate() proj[0] += f[i][1] * path[i][4]; // f.n proj[0] += f[i][2] * path[i][5]; // f.n } - if(com_flag == 0){ + if (com_flag == 0){ c_v[9] += 1.0; } else { for (int i = 0; i < nlocal; i++) @@ -710,7 +695,7 @@ void FixPAFI::final_integrate() /* ---------------------------------------------------------------------- */ -void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int /*iloop*/) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -724,7 +709,7 @@ void FixPAFI::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixPAFI::final_integrate_respa(int ilevel, int iloop) +void FixPAFI::final_integrate_respa(int ilevel, int /*iloop*/) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index 8de31f19b3b50ca2229e30853d82c09bd2aee2c8..5be9bf162b8fad4a448cdc80c797bd24c207f452 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------- */ #include "fix_pimd.h" -#include + #include #include -#include + #include "universe.h" #include "comm.h" #include "force.h" diff --git a/src/USER-MISC/fix_propel_self.cpp b/src/USER-MISC/fix_propel_self.cpp index 0a40177993b122b95e46121effcc2282b6ba8751..1b0d780c696a259650cae24ba3d3f737196afba0 100644 --- a/src/USER-MISC/fix_propel_self.cpp +++ b/src/USER-MISC/fix_propel_self.cpp @@ -19,25 +19,15 @@ #include "fix_propel_self.h" -#include -#include -#include - #include "atom.h" #include "atom_vec_ellipsoid.h" -#include "citeme.h" -#include "comm.h" #include "error.h" -#include "force.h" -#include "group.h" -#include "math.h" #include "math_const.h" #include "math_extra.h" -#include "math_vector.h" -#include "modify.h" -#include "random_mars.h" -#include "respa.h" -#include "update.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 612352aae185f0f9cbe57f7f431aad921ac56b8d..b088a86661fda1d7a6feb07e4a00defb8a87beb8 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -14,18 +14,17 @@ ------------------------------------------------------------------------- */ #include "fix_rhok.h" -#include -#include -#include #include "atom.h" +#include "citeme.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "math_const.h" #include "respa.h" #include "update.h" -#include "citeme.h" -#include "math_const.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index d110637b3c545cf1ff9b0396cd9587b6dd1cdacd..0dace284a9b8f657e9de6f6f943a01414bf34133 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -17,17 +17,17 @@ ------------------------------------------------------------------------- */ #include "fix_smd.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" #include "group.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index d61e7f1ee11194f3eefd662e05be546ffa66fe8d..97bf1fb07b312c9d7b1049f41da62811d0691198 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -16,19 +16,19 @@ ------------------------------------------------------------------------- */ #include "fix_srp.h" -#include -#include -#include + #include "atom.h" -#include "force.h" -#include "domain.h" -#include "modify.h" +#include "atom_vec.h" #include "comm.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "neighbor.h" -#include "atom_vec.h" +#include "force.h" +#include "memory.h" #include "modify.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp index ef7c4c02967fa3afae53f31bff8f6c9fddb2f334..bc10b5284cd80a5638258528f71c14e96ae3ba23 100644 --- a/src/USER-MISC/fix_ti_spring.cpp +++ b/src/USER-MISC/fix_ti_spring.cpp @@ -19,16 +19,16 @@ ------------------------------------------------------------------------- */ #include "fix_ti_spring.h" -#include -#include + #include "atom.h" -#include "update.h" +#include "citeme.h" #include "domain.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "citeme.h" -#include "force.h" +#include "memory.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index 8c37b19e8ba7d9798dddba1446bb8333a2494f5d..c12019528cc15309a41e559ffdbb04f51d1b64eb 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "fix_ttm_mod.h" -#include + #include #include #include "atom.h" @@ -32,8 +32,8 @@ #include "error.h" #include "citeme.h" #include "math_const.h" -#include "utils.h" -#include "fmt/format.h" + + #include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp index bd7e23047240c3d7161ab8555cc14f8f7b9b31db..c4be8b9f1b59dbda185009bfb66625ff453c1c43 100644 --- a/src/USER-MISC/fix_wall_ees.cpp +++ b/src/USER-MISC/fix_wall_ees.cpp @@ -16,13 +16,14 @@ ------------------------------------------------------------------------- */ #include "fix_wall_ees.h" -#include + #include "math_extra.h" #include "atom.h" -#include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "error.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.cpp b/src/USER-MISC/fix_wall_reflect_stochastic.cpp index 8afc506804454a35cfc9ae2d07f56e9cf6145473..9a8454b0173a94d8979aec55fde31e428c427bf1 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.cpp +++ b/src/USER-MISC/fix_wall_reflect_stochastic.cpp @@ -17,19 +17,17 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect_stochastic.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" #include "force.h" #include "lattice.h" -#include "input.h" -#include "variable.h" #include "random_mars.h" -#include "error.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/fix_wall_reflect_stochastic.h b/src/USER-MISC/fix_wall_reflect_stochastic.h index 0568dc8ae55a28a9f72ae35d838add461c3584ef..558ad7d084db213041fca021ec209cf52657b57f 100644 --- a/src/USER-MISC/fix_wall_reflect_stochastic.h +++ b/src/USER-MISC/fix_wall_reflect_stochastic.h @@ -20,7 +20,6 @@ FixStyle(wall/reflect/stochastic,FixWallReflectStochastic) #ifndef LMP_FIX_WALL_REFLECT_STOCHASTIC_H #define LMP_FIX_WALL_REFLECT_STOCHASTIC_H -#include "random_mars.h" #include "fix_wall_reflect.h" namespace LAMMPS_NS { diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp index 3a8323d58d32fd634eb8674502a49e4be4ae1be0..dfb11d6467c4e218507437ea78b5a65f8df6d31a 100644 --- a/src/USER-MISC/fix_wall_region_ees.cpp +++ b/src/USER-MISC/fix_wall_region_ees.cpp @@ -16,18 +16,18 @@ ------------------------------------------------------------------------- */ #include "fix_wall_region_ees.h" -#include -#include -#include + #include "atom.h" #include "atom_vec_ellipsoid.h" #include "domain.h" -#include "region.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" #include "math_extra.h" +#include "region.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 09cf7cf2c64fdc8df99e26a7848ebe5dfcfccdf5..57149312154eb13301545b645aa33afbd3a8f990 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_cossq.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 8ea58b23b303f7182b43bd8fbac460099d798660..476cf8ab43c558bd5d6866f4906ca158140b96c9 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "improper_distance.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 3bdbc7bc680cf79c1969843af3335ddc86522b3e..85f7809a028eb9f97fbda711089081ad53fd8b85 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_fourier.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "update.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 4102a250dd5c75d67876433964c6c4eee04a49be..c85e4850c839a899e237216a8ef814c94916ad99 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -37,7 +37,7 @@ ------------------------------------------------------------------------- */ #include "improper_ring.h" -#include + #include #include "atom.h" #include "comm.h" @@ -47,7 +47,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 764ccc587ff93c3bcc63f014bfec58802f182863..41f9bc953172bc11b656ae21ae21c1c986938d54 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -16,22 +16,20 @@ ------------------------------------------------------------------------- */ #include "pair_agni.h" -#include -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "force.h" +#include "citeme.h" #include "comm.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "citeme.h" -#include "math_special.h" #include "math_const.h" -#include "utils.h" +#include "math_special.h" +#include "memory.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 6a4575c6e4127831eaf32ab063f769f05133641c..9ef96f1188fb02bde50a7f46e411cd6400d5d395 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_mdf.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_cosine_squared.cpp b/src/USER-MISC/pair_cosine_squared.cpp index 8e400d23ed71925e55a03b0c748181a6214d8067..1203cea5f27caa935516babec014524d311d06fd 100644 --- a/src/USER-MISC/pair_cosine_squared.cpp +++ b/src/USER-MISC/pair_cosine_squared.cpp @@ -15,22 +15,17 @@ ------------------------------------------------------------------------- */ #include "pair_cosine_squared.h" -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index 14fbd374b68b96581d5caca3bb424db47fc296e4..5a3e12f1a5ed3800d539a45353ea1ff69748e9a7 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_diel.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 883796de1bc568411c144100d48d2038d9ae6ef9..44ab555b02121643738b78cb4f0471f2aa608702 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -28,7 +28,7 @@ #include "memory.h" #include "math_special.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_slater_cut.cpp b/src/USER-MISC/pair_coul_slater_cut.cpp index 194ff664b3294cd7b67720f3d1af9b70256ba546..5e799178c92520839e62a0e56cc11274942d925d 100644 --- a/src/USER-MISC/pair_coul_slater_cut.cpp +++ b/src/USER-MISC/pair_coul_slater_cut.cpp @@ -15,18 +15,15 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_slater_cut.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "memory.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_coul_slater_long.cpp b/src/USER-MISC/pair_coul_slater_long.cpp index d801d0342ff68fa0885f6546fd8e18b80468d580..0c94254f481884f523000e98adb346e4447173e5 100644 --- a/src/USER-MISC/pair_coul_slater_long.cpp +++ b/src/USER-MISC/pair_coul_slater_long.cpp @@ -15,23 +15,19 @@ * Contributing author: Evangelos Voyiatzis (Royal DSM) * ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_coul_slater_long.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "update.h" -#include "integrate.h" -#include "respa.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neigh_list.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_drip.cpp b/src/USER-MISC/pair_drip.cpp index cc890f8c94987dd333e5b81710c3a5e710cfc729..7b56caa20586f17a21dce111190464f1028b58cf 100644 --- a/src/USER-MISC/pair_drip.cpp +++ b/src/USER-MISC/pair_drip.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_drip.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_e3b.cpp b/src/USER-MISC/pair_e3b.cpp index 2b58e4b1f802cae8c7527da836a7ff63e94ccc4c..a7ed0fcaad89185c40dc58e69cdf7321a57add93 100644 --- a/src/USER-MISC/pair_e3b.cpp +++ b/src/USER-MISC/pair_e3b.cpp @@ -15,7 +15,7 @@ ------------------------------------------------------------------------- */ #include "pair_e3b.h" -#include + #include #include #include diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index bb9c7422120207b61efce4a692d25ba5fa07f29e..6ccaded35daaf7f5896dd0a958e26ffce641f79f 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -22,10 +22,10 @@ ------------------------------------------------------------------------- */ #include "pair_edip.h" -#include + #include #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -35,7 +35,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index 90a3502eaefc14f6862394776ac1575a033f0b56..4a81a41a260a5b9bf8be046357e62d3eb77002a1 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -18,9 +18,9 @@ ------------------------------------------------------------------------- */ #include "pair_edip_multi.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -31,7 +31,7 @@ #include "memory.h" #include "error.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 8f8d539679a99f3e090337e7ce6c4a228f1bbcb1..0db7f8739aa8d8a689bb992ebb38f6c5eeda7da2 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -16,9 +16,9 @@ ------------------------------------------------------------------------- */ #include "pair_extep.h" -#include + #include -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index 38d4c4d4c23b49b617273de633205fc071a4f967..c9601c416ec90ce2dd62f5607b2f349a8c983615 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gauss_cut.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index 62101d0e800d6871c936e2908fd2a030053936bd..671dcb309dd3ca61723959e9c6a74700c969cb6d 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_ilp_graphene_hbn.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -34,7 +34,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index fb1da5dab8a8e609c5489593dfe65f3fbaf282b3..9f986fa101fc19f2dae7249fad64a602eec4b3eb 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -22,9 +22,9 @@ #include "pair_kolmogorov_crespi_full.h" #include -#include + #include -#include + #include "atom.h" #include "comm.h" #include "force.h" @@ -34,7 +34,7 @@ #include "my_page.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index f02423e95215527f131bfc2cc384c1fd8d31cc25..7ce6f8652a29d001492f2e976eef189d0213552c 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -22,9 +22,9 @@ ------------------------------------------------------------------------- */ #include "pair_kolmogorov_crespi_z.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp index 5a84882cd900826bdad5d9cd101ca02175ca5c82..b8f9e5c38f19038c84fe5f888b5e670da6a95f03 100644 --- a/src/USER-MISC/pair_lebedeva_z.cpp +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -23,9 +23,9 @@ ------------------------------------------------------------------------- */ #include "pair_lebedeva_z.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -33,7 +33,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index 6faa599d2c30299feaac215c2ac5d1e2cb066368..31d32db505ba9a888bed318cdd67b6c2611b1147 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lennard_mdf.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index c553e671cb9edbd2859b959b2d767e2ac3c143ad..a93e0a81af6af3c915804b40dede30eea32a112c 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_list.h" -#include + #include #include #include "atom.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index 20081fa1e10cac873ebac0db90a521ae1bd13aa0..92e869e58c345293db63979b5582bb7a4f618004 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand_coul_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index 22f20a690e3e65d5b495a578eb1a90a319046bfe..baa0e233f226f9cc08e9683d6fd850b38be65b46 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_mdf.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index 6a92602683f1be2cbd0e48f1ecc2d196dd97e4df..ab845e69d55f01d4bcf136c6663cd5fb372d4f6e 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_sf_dipole_sf.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "update.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_local_density.cpp b/src/USER-MISC/pair_local_density.cpp index 8ad9793f98700c18fe58dfa6a328737e215c30cc..404f6e2db1d8fdcaeac6a9e72b48639c2042a8cc 100644 --- a/src/USER-MISC/pair_local_density.cpp +++ b/src/USER-MISC/pair_local_density.cpp @@ -18,22 +18,17 @@ ------------------------------------------------------------------------- */ #include "pair_local_density.h" -#include -#include -#include -#include -#include + #include "atom.h" -#include "force.h" +#include "citeme.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" #include "error.h" -#include "domain.h" -#include "citeme.h" -#include "utils.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 6091b95837fd0b7900dccea25a9094fa657a84b6..4d9b3866b768aa9dadd90f1ce222b9a2f6fc51ce 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -33,7 +33,7 @@ #include "pair_meam_spline.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -43,7 +43,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index 34cbe825817670f738ebed93b6fe57130ad8f67c..0a8aae233a41b18c9a2499687822f8b876568aa6 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -25,7 +25,7 @@ #include "pair_meam_sw_spline.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -35,7 +35,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 534f4acff5715d2823a0254008aed91b5fe1e79d..d534284b578ef8b9bfb44e702d74f79a4bb77052 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_momb.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "citeme.h" using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index 399723e0c5653dcd754c3c5e654507acd5271806..9f895800df6c58830271330ebc19b400e6c9fa58 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse_smooth_linear.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 9926318597753a8438793884782045f52abb5037..150895108e805e535cd7bfca564e0713d6397571 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -26,9 +26,9 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). ------------------------------------------------------------------------- */ #include "pair_srp.h" -#include + #include -#include + #include #include "atom.h" #include "comm.h" @@ -44,7 +44,7 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "thermo.h" #include "output.h" #include "citeme.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index 4df172a0018bc85d39c420eca3bfa6dbcc56f00a..1f5cfddff162891ee6f034b4e00cedecdd3dfd2d 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_tersoff_table.h" -#include + #include -#include + #include #include "atom.h" #include "neighbor.h" @@ -32,7 +32,7 @@ #include "force.h" #include "comm.h" #include "memory.h" -#include "utils.h" + #include "tokenizer.h" #include "potential_file_reader.h" diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index e4cab277c13daf4324011e6145bf3726322ffbfb..69f4559cacd24573a22774c415dc7e0f6831869b 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -18,22 +18,23 @@ ------------------------------------------------------------------------- */ #include "temper_npt.h" -#include -#include -#include "universe.h" -#include "domain.h" + #include "atom.h" -#include "update.h" -#include "integrate.h" -#include "modify.h" #include "compute.h" -#include "force.h" +#include "domain.h" +#include "error.h" +#include "finish.h" #include "fix.h" +#include "force.h" +#include "integrate.h" +#include "modify.h" #include "random_park.h" -#include "finish.h" #include "timer.h" -#include "error.h" -#include "utils.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index aa56ababe155daf91a7a0800f20f88ca204b2229..7ef134405def640ffa6b5f32ae8fd9e99a1c6aaf 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_class2_p6.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 0f49882e83a65fe4637f33b9e9c3ed89009d8f64..1bede58751d2fa73cd8855bc6c7a41ac592f43c7 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "angle_cosine_buck6d.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -28,7 +28,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 0ecc60ecc16b0c77dddbec2931b1bffeeefcfd6d..bbe6e48a352ab28cf5e9b453df60314774b8f83f 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "improper_inversion_harmonic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index 28fc9554488b88133692c24abcb32623a67c26ea..0de5423d30174328cbeed628b52a9aff7e21898e 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -29,7 +29,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 20bf7fa0498565080aa2ffa7e0a9abaf0ea94a92..c6ba832fff44398fb29ebace665628c97652ef42 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck6d_coul_gauss_long.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "math_special.h" using namespace LAMMPS_NS; diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp index d9d8ec3c97aaa9de218508454c6c38cdfda663bd..e0e92f9339c25fd868d5f7ed2333c61f3550487f 100644 --- a/src/USER-MOLFILE/dump_molfile.cpp +++ b/src/USER-MOLFILE/dump_molfile.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "dump_molfile.h" -#include + #include #include #include "domain.h" diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp index 798beaee096a68a0b4200219e81e7373532c3ba0..90a5781fff856ac11aacbec2f88436a295e88aa9 100644 --- a/src/USER-MOLFILE/molfile_interface.cpp +++ b/src/USER-MOLFILE/molfile_interface.cpp @@ -16,10 +16,10 @@ ------------------------------------------------------------------------- */ #include "molfile_interface.h" +#include "molfile_plugin.h" #include #include -#include #include #include #include @@ -31,8 +31,6 @@ #include #endif -#include "molfile_plugin.h" - #if vmdplugin_ABIVERSION < 16 #error "unsupported VMD molfile plugin ABI version" #endif diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 292a451a870b45bd1858dda76ea702a0956cbb2b..d26a4d4ba01b8cdb0ddca7c2db151db652094dc7 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "reader_molfile.h" -#include -#include +#include "molfile_interface.h" + #include "comm.h" -#include "memory.h" #include "error.h" - -#include "molfile_interface.h" #include "math_const.h" +#include "memory.h" +#include using namespace LAMMPS_NS; typedef MolfileInterface MFI; using namespace MathConst; diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index bb85dfb78402a1d8596082a825113062ec14461d..f936de6d02fbd9206c85c7258e56c16db6b3b24b 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -18,7 +18,7 @@ #if defined(LMP_HAS_NETCDF) #include -#include + #include #include #include "dump_netcdf.h" diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 8747bbea25506f7fb395dacb11b28e4c98529d66..19b06329220fbb64fa8a45d13b9d9eef651e7a6f 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -18,7 +18,7 @@ #if defined(LMP_HAS_PNETCDF) #include -#include + #include #include #include "dump_netcdf_mpiio.h" diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 6933afdcd9217760341f271ac202534f63293404..abc23367b18529b8c978b8ec3a513df128281098 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index 09ee59d5af6abc86c1d6f92dfdb2538c49dd04f1..b33b1c2e2f26e9cdaae57515298a17a9e309a827 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index ca5afe1449c00adf753caa21b46adb923ac681ee..0c209d3fe5b1d6eb6c73ec895d40c4f5ec35f7f2 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 48fdd9ba60aaf10f72875aa5582fca4faf139e02..cbeb10e08c791caf438d909326c7ef8832c979fa 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index a0e45fe1314591b46431cb6b4b286c0b9e46f904..b59046031ac621a065f6b363d7427cb3f634963f 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "math_special.h" #include "suffix.h" diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 21019336b3e90e096cd8f41317be9255faebd395..4870e6a3bb49a513759bb8226afb1a3862bb0991 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 1e6d712b628e718365c352c817be486da6b2ad8d..bec65caf6d52b97ffac676ded6a718053e0807cc 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index 6df1e028a039c04a8c5fbfc94264a31cbf36f660..dced90a967c1d67c4312853d07c36af3e774e92d 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index 26d8a7817e13ae326794350b67f6f8949dcbc84f..cea707161f3ed334b65fea839821a5828c17f0f5 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -23,7 +23,7 @@ #include "error.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index b6ddea3ff9ac3100ee8947ef6b40e458112c6f0d..ec9236902c7283ef414f4df978bd21caaf02f0ae 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index 992acf7c99fd58c7ddff8a88c223c7755d8ac3dc..774f06f80929759efa673258969138b1ef31bfd4 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 0cfc6f95af2740535723dbde84ff6456b90cdb60..5c81e3cba4b93e5e9655c3c333abd44cdeb796c9 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index a774edb8c46740145a55ee18b5964e29db935501..d6e9285f11a5e45c4a8888b9c8057190bc836e65 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index e0bc021f1b1bee68a01c00392069e29b97bc3e54..45d6c83aa1f32a6a35228b3f6bb5883320ac99c8 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -20,7 +20,7 @@ #include #include "atom.h" #include "neighbor.h" -#include "timer.h" + #include "comm.h" #include "force.h" #include "lj_sdk_common.h" diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index 1af60f85f651545591c0151185204d3f4a7d6b6e..f67d34017696984dd1a5ed7b63dd2c307b72859d 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -22,7 +22,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index 06edf46024be4f96f6a46501c2069c2cf1b80754..9c52bdb281887b1881cc78acb6ea19213bd34870 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index 5f3dd48841bee142df9faba768e1e9dbaf73b40a..38df4f50dacb0606ba09a70aea3322e99521d31b 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index ebf5afdc57e91bab9615cb66779659a9e66830b8..5dde355a767ea784abf37c546da3270fbe7371cb 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "error.h" #include "update.h" diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index d4d2d256019f6386b81fbc52c30358f5120ea6fd..012737f77d75c8809f25c346c948bce96daafae5 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index 9160ee70232e1f20a53fb3753ab1e621ecba4bf6..e8f17d5eae4d3544d1625b9b9ae22c74a933ee8b 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 7a6c616e4ae1f7ba5e215c9266ee780ccb322ed0..61a60fa995a7b4ad931620ff31240602f0f093c9 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 19f0a08510f57c7cb41caee1e400a31739a5b19f..50b4ed98a70553dd856fdd0fe1e753625127d9eb 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index 90318c8faf7939819a3ada85108d5e312a4e5ee1..51586370f5b3f965af7531410a57d45d16d14d4d 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index 809950f2b7e294d0624c8b9835db9ae58c753b40..720d660eae93f19791e0341edc2d97068eae661d 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index 0efaa10e3711d7c7d50d8e664b781c90d86383f3..bc1ae96ac99f8a1ece8b85d8502233af140af298 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include "pair.h" #include diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index f503bcab2622a813d2779f39047461f479b85fd6..3ccc65441acbd3500d66a6e4f39a7238a76abc1d 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -21,7 +21,7 @@ #include "comm.h" #include "force.h" #include "neighbor.h" -#include "timer.h" + #include diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index afd3071434c3929f028c449bdb77e387abe831cc..8454dc100457363be184eef205124fd5455e1d4f 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "pair.h" #include "update.h" diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index 49b8659e2facd64714fb83ecb184c5c09a0f6a86..cf65d735a6d1462053ad90c26b7ae4c4bb21bf6d 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index cea22adf1b4c3185fa3ab09ef93c1fe6379d8209..5d9164d3b3770d23d54ebd37bede8808a3ae8044 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 756931774a01733b1eb263f2be7421602e625b59..be19a6d9584f00a4c96f87fcba3aa5167331c7e8 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index d1f511954e0ecd5d702a782b8938f6739b5afa7c..3d51a4db43952f155c83b67400c8815907254c88 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index 5289fc2c6288f604cfe33cf42c5069ae8741c18c..5209fac23a83a2f87d131580b37be930a2faeef6 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "math_const.h" diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index edf8a20899d7482051c59edc40a3afdefb8c1f04..a6e0ab66d6da580a2d6a6044786732f1e711e7e4 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index bf51a0171377e0fe61250766bf297aa5402efad1..4604771912f56d79a8ddf5236bf4a7d5bde0ef79 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "update.h" #include "error.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 8814d3f3f04e41ff14e943fd4c63a5b1bc9bf810..ff0f6bb12b106d0ea768958f5f8495c75df33c61 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index e61c5f0d85cc4cf39df1180863d9f471f479e37c..5ffb8d64f2952d274ea1f7e67ded0d645a4f1fd6 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "update.h" #include "error.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index bf5332a1c1adac2b4ccac62818010626b7262630..c18d5fb4c0b9a160c4cd252ce67634c4f829db9f 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -23,7 +23,7 @@ #include "domain.h" #include "neighbor.h" #include "force.h" -#include "timer.h" + #include "math_const.h" #include "math_extra.h" diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index ec8d708da28c48c642da3c12af2b54a6a04498bd..d5480d2a9f5895a27513a7e0774160e1eab8258d 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -15,18 +15,18 @@ Contributing authors: Roy Pollock (LLNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "ewald_omp.h" -#include -#include + #include "atom.h" #include "comm.h" #include "force.h" -#include "memory.h" -#include "timer.h" #include "math_const.h" - +#include "memory.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp index 9c7317bebd192a5fcf41b6d7db21ec11fecae857..26cad769ec24e22249fd27e662bab93a79fb76fd 100644 --- a/src/USER-OMP/fix_nh_asphere_omp.cpp +++ b/src/USER-OMP/fix_nh_asphere_omp.cpp @@ -15,19 +15,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include -#include "math_extra.h" #include "fix_nh_asphere_omp.h" + #include "atom.h" #include "atom_vec_ellipsoid.h" #include "compute.h" -#include "group.h" -#include "memory.h" #include "error.h" +#include "math_extra.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 47757c4ec36186c94716e9a4fc859f2b3277ba82..f3c86a77462fbff0151071431665d983fc573759 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -16,7 +16,9 @@ OpenMP based threading support for LAMMPS ------------------------------------------------------------------------- */ -#include "omp_compat.h" +#include "fix_omp.h" +#include "thr_data.h" + #include "atom.h" #include "comm.h" #include "error.h" @@ -25,10 +27,6 @@ #include "neigh_request.h" #include "universe.h" #include "update.h" -#include "timer.h" - -#include "fix_omp.h" -#include "thr_data.h" #include "pair_hybrid.h" #include "bond_hybrid.h" @@ -39,6 +37,7 @@ #include +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index b0573dfa971151ce4aa05d2c3ef56dcf2f0f7e84..5b2ee884200ae5ba477dd6c4a7576f9549baabfc 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_comb_omp.h" -#include + #include #include #include "pair_comb.h" diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index a10d3127a9a9c7992ca61c4b931a2c80e320d86d..ef0f918cbf595a4e51fe2aa98304f7039ba81a5b 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -32,7 +32,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax_omp.h" -#include + #include #include "pair_reaxc.h" #include "atom.h" diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp index 63084fcc9ef023f38f844b71d3c2b2efdd913514..d56b633bd049f6c4c81d7d1693a13676cfbb1b2a 100644 --- a/src/USER-OMP/fix_rigid_nh_omp.cpp +++ b/src/USER-OMP/fix_rigid_nh_omp.cpp @@ -15,10 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "fix_rigid_nh_omp.h" -#include -#include + #include "atom.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" @@ -29,18 +27,20 @@ #include "error.h" #include "force.h" #include "kspace.h" +#include "math_const.h" +#include "math_extra.h" #include "modify.h" +#include "rigid_const.h" #include "update.h" -#include "timer.h" +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "math_extra.h" -#include "math_const.h" -#include "rigid_const.h" - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp index 9f78f6dc260c687d19d163d1d76c168f01c1a28d..62f853d23b497f975c7d6443db6743201e05c79e 100644 --- a/src/USER-OMP/fix_rigid_omp.cpp +++ b/src/USER-OMP/fix_rigid_omp.cpp @@ -17,7 +17,7 @@ #include "omp_compat.h" #include "fix_rigid_omp.h" -#include + #include #include #include "atom.h" diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp index 227b0e1f8a9a0f1c40a79aa3300f181f16d93d29..f720dd617eafe57b5e44235558e7bae46bedb6ed 100644 --- a/src/USER-OMP/fix_rigid_small_omp.cpp +++ b/src/USER-OMP/fix_rigid_small_omp.cpp @@ -24,7 +24,7 @@ #include "atom_vec_tri.h" #include "comm.h" #include "domain.h" -#include "timer.h" + #if defined(_OPENMP) #include diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index 8927980951443a29167349f1b7aa4ca3a9e631b6..05fc8e44756323c2620d58e5f7355077e5a73bcc 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 72d76e8c42190cf54ead303aa64af4d51f284713..e2a43c58c4132b5156f7f803f880d208542e7522 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index e9ff4bfc73e0a23fd694641689761188170238c5..715819cfb92e2410d1c2c062d308244a80b3f374 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index 0671bdc375335ab6b2478438a94e813634106cee..93dfb9bc992a097c8379d7771f99a7ca79e5e92d 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -15,18 +15,20 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "improper_fourier_omp.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "timer.h" +#include "error.h" #include "force.h" +#include "neighbor.h" +#include "suffix.h" + #include "update.h" -#include "error.h" -#include "suffix.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define TOLERANCE 0.05 diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 8bef42bf23bce154e9acf3af9a13d6af8ee4382c..6bb76871b2975ad46f2a9f5a1127f8c760f11aa9 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index 4ba67aab700787be50722f3aaff6d94123e71708..51ea5e5198e796340e75501089fe86a8daeeb005 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -15,17 +15,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "improper_ring_omp.h" -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "timer.h" #include "force.h" #include "math_special.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index bf466afb19a8f8ff554a9bb9e888bc6abf717222..0c9befade6a34076571e8901511383b1e1bfa84f 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -21,7 +21,7 @@ #include "atom.h" #include "comm.h" #include "neighbor.h" -#include "timer.h" + #include "force.h" #include "update.h" #include "error.h" diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index 524850eb634556d897c89ab88e078ace181f2f17..c42aa8e0c14f7292f7ca584eac4a1e25ec9d7798 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -16,24 +16,24 @@ Original MSM class by: Paul Crozier, Stan Moore, Stephen Bond, (all SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "msm_cg_omp.h" -#include -#include -#include -#include #include "atom.h" -#include "gridcomm.h" #include "domain.h" #include "error.h" #include "force.h" -#include "neighbor.h" +#include "gridcomm.h" #include "memory.h" +#include "neighbor.h" #include "thr_omp.h" -#include "timer.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include + +#include "omp_compat.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp index 26892267253c735e9f49bae854f97ee85c6c55fa..783ebb40f1eca31a065b833de1b01d734040ae9f 100644 --- a/src/USER-OMP/msm_omp.cpp +++ b/src/USER-OMP/msm_omp.cpp @@ -15,14 +15,15 @@ Contributing authors: Axel Kohlmeyer (Temple U), Stan Moore (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "msm_omp.h" -#include + #include "comm.h" #include "domain.h" #include "error.h" -#include "timer.h" +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 63a539c93c7ac3806ec9e4da80c031ff7290af3c..97d94e55130c1fa65989ee1527844a5341d6b416 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -12,19 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_adp_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index b61bf52e4ee8009471d902a56e2f6a58aa7e1f3e..de6903aab90617456b42a75405a9715f8db465b8 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -12,21 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include -#include // requires C++-11 #include "pair_agni_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "math_special.h" #include "math_const.h" - +#include "math_special.h" +#include "neigh_list.h" #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_airebo_morse_omp.cpp b/src/USER-OMP/pair_airebo_morse_omp.cpp index 5d5ac0b885bfaeccd9f714d7c3130d94d583784d..6977842af211cb7a86cc014f59bd95266de054e4 100644 --- a/src/USER-OMP/pair_airebo_morse_omp.cpp +++ b/src/USER-OMP/pair_airebo_morse_omp.cpp @@ -12,8 +12,6 @@ ------------------------------------------------------------------------- */ #include "pair_airebo_morse_omp.h" -#include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 25d6c35174f0282730457f8bea3a1d964bf6c210..837734d6e493cde3f6defc3c55d9d151571da933 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -12,24 +12,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_airebo_omp.h" + #include "atom.h" #include "comm.h" #include "error.h" -#include "force.h" +#include "math_special.h" #include "memory.h" #include "my_page.h" -#include "math_special.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" + +#include +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index bb41334153a0dace309f964afe4b2438d3601aa9..01e33dc5c519d791d4a27c28ae4ed5d5ae738b64 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_special.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp index 7f92ab6734b60470b3bf327bfbc8af9497c8f17f..b410c998e10139b113b4f43e4de48464d694b549 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.cpp +++ b/src/USER-OMP/pair_born_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_born_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp index eec17658597179e267d7532564b760da6bfc1aa1..4adba396e8c6199a59b492c6c6e2e76b6f59efc5 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_born_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index ffa069ec4e62b87d0912f5b89da55c84684cc102..9bc6507c6a5fe78d221205b41f009f3d3cb011f7 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_const.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index aaac28d07cc7a00c6d5f6db8e16d8b71216debb0..e74f0139c18d6ba050a84f23ce467ce069b21663 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index ca28fa14bb4c32a396d46582eab9651b59079711..b7b82c3dac1ab38c059020a339cb8f4a22e9b1c9 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -12,26 +12,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_brownian_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" +#include "math_special.h" #include "neigh_list.h" +#include "random_mars.h" +#include "suffix.h" #include "update.h" #include "variable.h" -#include "random_mars.h" -#include "math_const.h" -#include "math_special.h" -#include "timer.h" -#include "fix_wall.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 939bc223eb6642457c403a2254b239e2c217dbb1..4d8b4572810f727a68a06066d4ebfcf9dc48624e 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -12,25 +12,25 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_brownian_poly_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" +#include "math_special.h" #include "neigh_list.h" +#include "random_mars.h" +#include "suffix.h" #include "update.h" #include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "math_const.h" -#include "math_special.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp index 4154c1281c94514153dd45478c419e0e61cb81d1..1c433f8083825b954209c7af307729620edcdd24 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp index 1be2b7272fbf08a422e57d5f99e95a1a4c88316d..264073a07e507f093e5f1befc6e7ca1441ef7ec3 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp index b26243b19afe6ad311f3a32edb700b92261078c1..631a1ee61d90d97b04d8f6cc7184d4ba4dc4a66c 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_buck_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index a2e34b9a1bfa401b0952cf2c8362fc7a689a4c84..00ab1c248c571085c81f95a0f6c1c1389bc45f3e 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -11,18 +11,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ - -#include "omp_compat.h" -#include -#include "math_vector.h" #include "pair_buck_long_coul_long_omp.h" + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" #include "force.h" - +#include "math_vector.h" +#include "neigh_list.h" #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index fc85d79c81efabff1cf752df9afe086319c8d046..bddacaf5b5cc2efe5888fafe632ce987fc93b42e 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp index cce588f51694eaf33fc118b31d24efa84fe3df09..94325232fcbfb174215deab3bcf1c48209ade5ce 100644 --- a/src/USER-OMP/pair_colloid_omp.cpp +++ b/src/USER-OMP/pair_colloid_omp.cpp @@ -12,18 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_colloid_omp.h" + #include "atom.h" #include "comm.h" #include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_special.h" - +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index 8912cbc2432d35140c4d4791f054c308384b8548..9a0155d6d38cb6528789c50f616971c783a297b2 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -12,19 +12,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_comb_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "group.h" -#include "force.h" #include "memory.h" #include "my_page.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" +#if defined(_OPENMP) +#include +#endif using namespace LAMMPS_NS; #define MAXNEIGH 24 diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index 69eb9ac0f3a99d582f72081ea8032962145c6675..57b821cb8bc71d76bbbd6a1a023b460e82203e65 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp index 89222903ec8d7bf89cfad2f23abcd1d31a13c0dc..f8b3a36e394cea86c9f8fe423ff091d0f98906b3 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index c22f7340c4f1602f8d21a13d680672ad815bba2b..1bb8676998d17ba757171c361ccfc6deab3cb0bf 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp index 656cdc9421f6b71dfd9684fbb5ac647700223f97..62f258042681edb5c92255eb1c09eff0499b1402 100644 --- a/src/USER-OMP/pair_coul_diel_omp.cpp +++ b/src/USER-OMP/pair_coul_diel_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_diel_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index ddcc8dbeb08d423636efa38adca8bccaa4cda3cb..3a8db4563498b2f67cf2941167ccf75c03e16a0c 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -19,7 +19,7 @@ #include "comm.h" #include "force.h" #include "neigh_list.h" -#include "timer.h" + #include "suffix.h" #include "math_const.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp index 6c9b9d034d0f22caf1de10c277bdae4d5daa8fde..92cb51f7a484346eb11adf2c13241c8e7b995d2f 100644 --- a/src/USER-OMP/pair_coul_long_omp.cpp +++ b/src/USER-OMP/pair_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp index ff3267fb38cd44927cf94f351b14fe32640ec82f..28ba13d5cfb8019c27f9d6f3a5a64ef4b1cf309e 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp index 32a657e2867d5e56c44ae8deb2cb4d88f7249086..e907d63eb17d27796e0fc7bdb858c24bc1f0b3a7 100644 --- a/src/USER-OMP/pair_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index d0f6fdb1255ad72dee20593a2b66afd4c57ab811..71e8148a50e19714967756b5def81eb0e4e82262 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -20,7 +20,7 @@ #include "force.h" #include "neigh_list.h" #include "math_const.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index f3a1c29a707068463b01d5476d72f44103a37d69..6e3da77cbe6bb8164d586998f6fce380839822df 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "update.h" #include "random_mars.h" -#include "timer.h" + #include "suffix.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp index 06e80274bd9797968267a64b89cc0672fc89b40e..823367109b2ec8550fbc1f0dc310c4d0baa6a62a 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.cpp +++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp @@ -12,18 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_dpd_tstat_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" -#include "update.h" #include "random_mars.h" - #include "suffix.h" +#include "update.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EPSILON 1.0e-10 diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp index 3e0e423f3dbb3b33bcc02bf622b09e0764d2b0b7..c7559420bc06800657da9b157d162d1e410157ef 100644 --- a/src/USER-OMP/pair_eam_alloy_omp.cpp +++ b/src/USER-OMP/pair_eam_alloy_omp.cpp @@ -15,18 +15,16 @@ Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_alloy_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp index 76e9840a5c6e022020111cf1c95466b88981a85e..66a7581c218f5d936158a11346560b68ff43c7d9 100644 --- a/src/USER-OMP/pair_eam_fs_omp.cpp +++ b/src/USER-OMP/pair_eam_fs_omp.cpp @@ -15,18 +15,16 @@ Contributing authors: Tim Lau (MIT) ------------------------------------------------------------------------- */ -#include -#include -#include #include "pair_eam_fs_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "tokenizer.h" +#include "memory.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 60ae65def562e3587428288a05de1d27694493b1..e6ba299a4d84d8a0e56c959471dbcd290814a7a0 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_eam_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 0e59674b0e5fbc0347e1f6570af3a64e3a0af423..864ff68f7a375bb3380b85880036f82ea6435b48 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_edip_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" using namespace LAMMPS_NS; +#include + +#include "omp_compat.h" #define GRIDDENSITY 8000 #define GRIDSTART 0.1 diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp index 02b765a956a5113ce39598a8952ccacff4e981e7..74b460a788b28d621c7d1052c54b3b261506319e 100644 --- a/src/USER-OMP/pair_eim_omp.cpp +++ b/src/USER-OMP/pair_eim_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_eim_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp index 6d5344701d914a3bd2928da9b29053118ea759eb..a453915738fb3aea8bcad21c2a5650957c7cd05a 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.cpp +++ b/src/USER-OMP/pair_gauss_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gauss_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp index 103a76661418415c4ebce98f7320cb4d341cbaf9..3e5777e4ecccc4a6cbe2f67a43263ac6865e2452 100644 --- a/src/USER-OMP/pair_gauss_omp.cpp +++ b/src/USER-OMP/pair_gauss_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gauss_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EPSILON 1.0e-10 diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp index f0fd60a3096353f55906b3a241787a632c6d3328..991c72a9be0b9e590af9936aeaff13089fe39059 100644 --- a/src/USER-OMP/pair_gayberne_omp.cpp +++ b/src/USER-OMP/pair_gayberne_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_gayberne_omp.h" -#include "math_extra.h" + #include "atom.h" -#include "comm.h" #include "atom_vec_ellipsoid.h" +#include "comm.h" #include "force.h" -#include "neighbor.h" +#include "math_extra.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp index bb8bbcc98458f9e8e50a82e63c5ae6003382a50d..338eb5245330505546985e3e9d903b9da714c8ab 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp @@ -12,22 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_hbond_dreiding_lj_omp.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - #include "math_const.h" #include "math_special.h" - +#include "molecule.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp index 4ad3a8f057013904f3d5bf1e5fd51f2298427a5e..5094d5c1938a6def74c1f02e31359aeac4221587 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp @@ -12,22 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_hbond_dreiding_morse_omp.h" + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" #include "domain.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" - #include "math_const.h" #include "math_special.h" - +#include "molecule.h" +#include "neigh_list.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp index adf0aac9b20c4555a6b13165a0e699d801c1fcb4..5aeec25d13d334834c47e99ed46ca712ded7021d 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.cpp +++ b/src/USER-OMP/pair_lj96_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj96_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index f357fd9068b17b9038f4995913dc9b70edfb39a0..3ff02b61093a57480a94c78d49479a74b4ccca79 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_charmm_implicit_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp index 55227e2e100921711479906d69a84aa1737d35d1..77caf63f18dec62c33fb2a7766795a514d949e20 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_charmm_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp index 437bd183ed5c948fedaaa581e3cb2dc91203bf4a..56cf0a68dd5fdb10250d7eb770e476134cb19e84 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp index b32f108098d6cad14ed1581d88b948514c7e2a66..e19632dc7ef8c7f5005c93b02b8deb09c2b0c181 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp index 0000e63cda7e1dc17e5decc48d3bae17fe4688b3..a39ef0aa81d7f3b1b58b5acc277b2ded5a92787b 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_charmm_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp index 59a6841c9ef6e3acdbaf858cbe67b274fc07ad18..63fb4fe52978910fba7b4f8b5c7195f69c195964 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp index 480e2adae011e56cc29ff5db469969243131607b..f618f7f423b8c1db2bfd3ac4393aac4f3a9c195c 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp index 2b91e10cfa9a86002c7ef4b2de5df109cd107366..39cc320e44934c4e396df5315fa6c2bb335ad6e0 100644 --- a/src/USER-OMP/pair_lj_class2_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_class2_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp index 778c25393d37f1cf8c9b599aa1e487164d3c6cd6..27f6132491e43966fa150f6034f20b179cb2de6c 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.cpp +++ b/src/USER-OMP/pair_lj_cubic_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cubic_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace PairLJCubicConstants; diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp index d560b803f1650dec75b2967292b314b7238392d2..2f46e0bfe70789c68e4e2a5f74bf0ddd55adca64 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp index 1c88600e7a6970e4782ad8df6ba70264898510f1..03f0852b064348945ef56955825e4aaacb1aeab0 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp index 79754e704b2c8e3b15b584883a12f3b45fc48f01..82031f91ab82943dc8c9330958e74853d10816f2 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_debye_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp index ec69a1a1ca92d332c11b2f3989d2084b63aa8f58..7ab6f31b3fa523aa0d577b55ee829c9ec82366ce 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_dsf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" - #include "suffix.h" -#include "math_const.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp index 618986389c799f1ed6ad1011a256212b8894b8ae..c7b6de80226a382a53849193a29873968f118c2e 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp index ce84ba01c3baf76d44d914b9723a45ee959baeec..6e804bd8aebb159a3b21e5e2d6fbd975ee3e2bf9 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_long_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp index 58e5cee0c21857d98d18dc9363eb4d1586d27a8d..0e6d11327afcfe70150b18bf4bfedcfbe8ce7e23 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_msm_omp.h" + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp index 4111c5b22c122e34cf9e99fac9669f1cbfe561fc..0e9a333121a9adf8cb4d221992b204a0bd36702c 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_coul_wolf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" - #include "suffix.h" -#include "math_const.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp index 7d5d25c39bf622f119fdbcf4aff16e2b85c9c1d4..2cc915a43532f3097a40cab8507c3680cf8f775f 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_dipole_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp index 3e7e92de21aed2e6fc0685698d5c05b5a7536885..2aa71026e3691acdec02e69f84fe250140738b31 100644 --- a/src/USER-OMP/pair_lj_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp index 5064c4705e8de478160ee43c031e3565a606a5ed..406c5f41d9ebb98c7d24634e759a25652e71c8cb 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp @@ -12,16 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_cut_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 72a7d5f16a293b9b12b75a131c42fc572a74fd5b..b921c8f1c169be70b06731bccef8a2236fa766d9 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -15,25 +15,21 @@ Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_lj_cut_thole_long_omp.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "fix_drude.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" -#include "error.h" +#include "neigh_list.h" #include "suffix.h" -#include "timer.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.h b/src/USER-OMP/pair_lj_cut_thole_long_omp.h index dc64c5c3a29eaa5f1653ffee87b75cdee6cac1f2..212f3c4e2ec8d76bef9efb6da23bd9a3bc852333 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.h +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.h @@ -20,7 +20,6 @@ PairStyle(lj/cut/thole/long/omp,PairLJCutTholeLongOMP) #ifndef LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H #define LMP_PAIR_LJ_CUT_THOLE_LONG_OMP_H -#include "pair.h" #include "pair_lj_cut_thole_long.h" #include "thr_omp.h" diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp index 70b5e436fa40655e1ab1617cb34fda64d04e66ef..89077ba6af6c22526ae886a8af8816209e962998 100644 --- a/src/USER-OMP/pair_lj_expand_omp.cpp +++ b/src/USER-OMP/pair_lj_expand_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_expand_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp index 0f0a8de2ff9872cc4a6a630a69eabd9c4fee0eb0..26a6e979b496a3b575b1fc8b665a99004f0deda6 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_gromacs_coul_gromacs_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp index ea2c9e8f557ac0111f4d33f1b6df1e33385bd376..308209153990e8f9046fb7847466dcb1be540399 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_gromacs_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index e74f48712969557f5aa0d067de387db8352d13a5..cdd62ff96eb691f7efc643a6ef9bd53168165eb4 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -12,17 +12,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_long_coul_long_omp.h" + #include "atom.h" #include "comm.h" -#include "math_vector.h" #include "force.h" -#include "neighbor.h" +#include "math_vector.h" #include "neigh_list.h" - #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index 9c8de110d7563dfc6173503343234120ca8984fa..af24e93a41ea8141a537cbff9b321d7f2e12c4da 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -12,20 +12,21 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_long_tip4p_long_omp.h" + #include "atom.h" -#include "domain.h" #include "comm.h" -#include "math_vector.h" -#include "force.h" -#include "neighbor.h" +#include "domain.h" #include "error.h" +#include "force.h" #include "memory.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp index 4ad082cde189e2f944ee9b10dc598e38db6ad21d..4a53f2c08326f11eafd93c9932cf576708ce18b0 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp @@ -12,18 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_coul_long_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" -#include "lj_sdk_common.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp index 4871356b184611c0750be2c29612f0ed46f0e8b9..4b89375b5b84c5c2d064275fe20880447e92a864 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp @@ -13,19 +13,19 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_coul_msm_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" -#include "lj_sdk_common.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp index 9f0671c61c29b02f4c2807c5a85cd205afd5a8c4..d5146c6798309d00b5cd791726a0600965506003 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_omp.cpp @@ -13,18 +13,18 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sdk_omp.h" +#include "lj_sdk_common.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" +#include "suffix.h" -#include "lj_sdk_common.h" +#include -#include "suffix.h" +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace LJSDKParms; diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp index 1adaf939531c8cb95ef5f6b6ec1b8b44225ca319..8828b40b98486845e40339f441662149915a6f65 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_sf_dipole_sf_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp index 497c2c3a4365b06d84aea4b1cb648b6c68f9f913..2c0c0281893b7e9c665496e8e158138d272f12ce 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_smooth_linear_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp index bdb9b3141e0940336bf1dde727d3efd8fb23e02f..0b4ea4e5f82172710138bc2ee70e688f623276a6 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lj_smooth_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index 9db42395870645edf1e6fa836e0337ac69fc70b1..caf5a11124e5821ab4dde9d422f3beed4fa9e788 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -12,24 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_lubricate_omp.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" -#include "update.h" +#include "suffix.h" #include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "fix_deform.h" -#include "math_const.h" -#include "suffix.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index dc143a316027c45fe299419a1aa887b99e319415..feb110194f55e0231619f8cd5f84c18efe57bd3b 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -12,24 +12,22 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pair_lubricate_poly_omp.h" -#include + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_wall.h" #include "force.h" #include "input.h" -#include "neighbor.h" +#include "math_const.h" #include "neigh_list.h" -#include "update.h" +#include "suffix.h" #include "variable.h" -#include "random_mars.h" -#include "fix_wall.h" -#include "fix_deform.h" -#include "math_const.h" -#include "suffix.h" +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp index 19fb09dd7b5ea992921ccde3f410be3783404a63..782371e843815205cf9493e534f503bf8fe5aa39 100644 --- a/src/USER-OMP/pair_meam_spline_omp.cpp +++ b/src/USER-OMP/pair_meam_spline_omp.cpp @@ -12,19 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include - #include "pair_meam_spline_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" +#include "error.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp index 1f566dbd42acd20af4bcb1d628150c1ef8c4408a..48687781ef70ba1f4049226b34f4c11aea9862b5 100644 --- a/src/USER-OMP/pair_morse_omp.cpp +++ b/src/USER-OMP/pair_morse_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_morse_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp index f2ab4170281cf9fd249c08ab7ecdd369b8722bc2..220fb9481d841030fa4a2ed58ee4a97197e25f7f 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp @@ -13,16 +13,17 @@ Most code borrowed from pair_morse_omp.cpp ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_morse_smooth_linear_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp index 4326434450b091148521e150252df0215ebacb65..1cfe576a32d796afde687a1299a83ba029fe03dc 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_coul_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp index 970b383f7e7de84272fcdb14e55c64af367c02d9..d9e123182703266f17c06e153974c7473043b40a 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_coul_long_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define EWALD_F 1.12837917 diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp index a937668fdd3831b9db410ae946e32592672e0e1b..a232da1a9017f4f6b2f9e30e07fff498a192e9a7 100644 --- a/src/USER-OMP/pair_nm_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_nm_cut_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp index cf29b5cab85994a35270d7522dc75ff2addaae83..9bf707ad91666b8144662f813ff82d365a375eb8 100644 --- a/src/USER-OMP/pair_peri_lps_omp.cpp +++ b/src/USER-OMP/pair_peri_lps_omp.cpp @@ -12,24 +12,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_peri_lps_omp.h" -#include "fix.h" -#include "fix_peri_neigh.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_peri_neigh.h" #include "force.h" -#include "memory.h" #include "lattice.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" -#include "math_const.h" - +#include "neighbor.h" #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp index 1990b46fe59407cf8c411375d2e489584268e053..28df45b67f0d2ca0eb3da8fdff33cc8c860fc58c 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.cpp +++ b/src/USER-OMP/pair_peri_pmb_omp.cpp @@ -12,23 +12,23 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include -#include #include "pair_peri_pmb_omp.h" -#include "fix.h" -#include "fix_peri_neigh.h" + #include "atom.h" #include "comm.h" #include "domain.h" +#include "fix_peri_neigh.h" #include "force.h" -#include "memory.h" #include "lattice.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 73b1373fad4a8c580e9bbb1f132a7fdaa22a43c7..dfc1f428eb81f8559d327db1808e9139fe837dc6 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -34,7 +34,7 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc_omp.h" -#include + #include #include "atom.h" #include "update.h" @@ -48,7 +48,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "timer.h" + #include "reaxc_defs.h" #include "reaxc_types.h" diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp index 557d212531b77e24907a772c3e8db586543641a4..689ff297e59d079ffc2baacad479d3883be49eb7 100644 --- a/src/USER-OMP/pair_resquared_omp.cpp +++ b/src/USER-OMP/pair_resquared_omp.cpp @@ -12,18 +12,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_resquared_omp.h" -#include "math_extra.h" + #include "atom.h" #include "comm.h" -#include "atom_vec_ellipsoid.h" #include "force.h" -#include "neighbor.h" +#include "math_extra.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp index 85425974cccdaacf66dcbed7377ea98b3076edce..f733b5106f5f492dfe6dc2662a275a826e9a697b 100644 --- a/src/USER-OMP/pair_soft_omp.cpp +++ b/src/USER-OMP/pair_soft_omp.cpp @@ -12,17 +12,18 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_soft_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" #include "math_const.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index ebe501ff8e359eb3b8ff10fb9d2786a5f269c189..c2eb4cb156949fb42f6b2d92c6120e0e61778ca9 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_sw_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp index 2546bfdc9a6ea9446b8442fd3c76831c03355c57..f5fbabccabb19eac9974a694bd0b97a1def7acab 100644 --- a/src/USER-OMP/pair_table_omp.cpp +++ b/src/USER-OMP/pair_table_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_table_omp.h" + #include "atom.h" #include "comm.h" -#include "error.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index 5e1e6b1b0e973482db8c994294be5536422fa391..83baa56e442ef36d9418cd04882afc6dbad6344e 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -12,16 +12,14 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_mod_c_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index aa90b883751c575bebffc0ab4338ebc8895a4def..ab2f07322de02ba4fc2a596a0f54eefefab2d3e7 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -12,16 +12,16 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_mod_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index 34dbfb73b6d92176d2ed8edc5fba572a99d73983..a3677499781cb4d70600fda4ba484486829926c3 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -12,17 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index a0a7f4c810e0e7ee6d5cc35efbd028b9d45302a5..8321ad9d9ffd2aa53d0b7d8b1f1b115b96de015d 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -12,18 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_tersoff_table_omp.h" + #include "atom.h" #include "comm.h" -#include "error.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; #define GRIDSTART 0.1 diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp index 005cd427a90f4996fc3eea50505b2c19e9eb508b..7bb38145499de7f06c0021a297d416adf2e24d30 100644 --- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp +++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp @@ -16,26 +16,19 @@ David Farrell (NWU) - ZBL addition ------------------------------------------------------------------------- */ -#include -#include -#include -#include #include "pair_tersoff_zbl_omp.h" -#include "atom.h" #include "update.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "force.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" #include "tokenizer.h" #include "potential_file_reader.h" - #include "math_const.h" #include "math_special.h" + +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp index 605d6dd2c6c6f81e4d82751a6f2b36128ee0396a..e1c2ff457ea7d28a731ccc18606c8d834964a126 100644 --- a/src/USER-OMP/pair_ufm_omp.cpp +++ b/src/USER-OMP/pair_ufm_omp.cpp @@ -14,16 +14,17 @@ Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_ufm_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index 425a06c296d0aa8bec1c65bc4be061349d0c89d6..0637fe3dfc6553d7f9f7040b22c8b6e48a128233 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -12,17 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_vashishta_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - +#include "neighbor.h" #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index 36c86a89953cd6f7adb97c14853c9602db949ea3..9650a57e725558bbb18033afb7e97ef5e5d293b9 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -12,17 +12,15 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_vashishta_table_omp.h" + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp index e6ac3fa9fbe5f77ba1b1cca37a6d6071a14f7dd3..227ec0744f3f4dcf06896e1a6e50f5e17bcd747d 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp +++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_yukawa_colloid_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp index f222876cb528f35447dc4697aae9622436318460..347575e2837ba8cb3a6b27272738b1bf7eecf8b8 100644 --- a/src/USER-OMP/pair_yukawa_omp.cpp +++ b/src/USER-OMP/pair_yukawa_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_yukawa_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp index 284ebbf09c6f9c04f760e8d13d807a2ddeca8ff8..9679a00b245de35de3e4e5e09b169d3c778c84f1 100644 --- a/src/USER-OMP/pair_zbl_omp.cpp +++ b/src/USER-OMP/pair_zbl_omp.cpp @@ -12,16 +12,17 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" -#include #include "pair_zbl_omp.h" + #include "atom.h" #include "comm.h" #include "force.h" -#include "neighbor.h" #include "neigh_list.h" - #include "suffix.h" + +#include + +#include "omp_compat.h" using namespace LAMMPS_NS; using namespace PairZBLConstants; diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp index 31098d2675c6a6ac79886f6e3f2952de85a8979f..86997713efa1e9effa78e3c61f11f92f5e4eb155 100644 --- a/src/USER-OMP/pppm_cg_omp.cpp +++ b/src/USER-OMP/pppm_cg_omp.cpp @@ -15,22 +15,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_cg_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp index aad77cffc72ff014cfe7fd40545f8a543a033303..96a2cc282e0d288a44c6ca9778e2e271c4809b92 100644 --- a/src/USER-OMP/pppm_disp_omp.cpp +++ b/src/USER-OMP/pppm_disp_omp.cpp @@ -16,23 +16,24 @@ Rolf Isele-Holder (RWTH Aachen University) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_disp_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp index 7da4257e07106bcd2831c2e2d3407f2b1ccf6ff9..93b7a87a6103cbd5f64391e86f637ddccb1a8901 100644 --- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp @@ -15,21 +15,24 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_disp_tip4p_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "error.h" #include "force.h" #include "math_const.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp index e3e46f4de07fc2c342975fef97b9215f3e55f85b..70655885260e5e106223a1afcc12c37d665a13b1 100644 --- a/src/USER-OMP/pppm_omp.cpp +++ b/src/USER-OMP/pppm_omp.cpp @@ -15,19 +15,19 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp index 8bd9805f019ca5f9249a4ae07088cddf850e4c96..936f3cf31ca28e6a2e356894fe4a5faecd3fca33 100644 --- a/src/USER-OMP/pppm_tip4p_omp.cpp +++ b/src/USER-OMP/pppm_tip4p_omp.cpp @@ -15,11 +15,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "pppm_tip4p_omp.h" -#include -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" @@ -27,12 +24,16 @@ #include "force.h" #include "math_const.h" #include "math_special.h" -#include "timer.h" +#include "suffix.h" + +#include +#include + +#include "omp_compat.h" #if defined(_OPENMP) #include #endif -#include "suffix.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index d581819e00bb8e1dc4f054e2fb6e05d65e7d5c60..85a77370faad1f0e220cbc056bc33866a2bf0b49 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -27,8 +27,8 @@ ----------------------------------------------------------------------*/ #include "reaxc_bond_orders_omp.h" -#include -#include +#include "reaxc_bond_orders.h" + #include "fix_omp.h" #include "reaxc_defs.h" #include "pair_reaxc_omp.h" @@ -36,6 +36,9 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_bond_orders_omp.h b/src/USER-OMP/reaxc_bond_orders_omp.h index 36be3337ad8a79d52998e139349c9c7fffc8e2ac..2027a8628eea6958904846852c9528c9097fc2a8 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.h +++ b/src/USER-OMP/reaxc_bond_orders_omp.h @@ -30,7 +30,6 @@ #define __BOND_ORDERS_OMP_H_ #include "reaxc_types.h" -#include "reaxc_bond_orders.h" void Add_dBond_to_ForcesOMP( reax_system*, int, int, storage*, reax_list** ); void Add_dBond_to_Forces_NPTOMP( reax_system *system, int, int, diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index ee4670fe59bbe637a4d89ba02c14944b4a602bb1..ad6ea35eb8780702fc7f66ff545e0e374f02c4b5 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -26,13 +26,12 @@ . ----------------------------------------------------------------------*/ -#include "omp_compat.h" #include "reaxc_forces_omp.h" -#include -#include + +#include "error.h" #include "fix_omp.h" -#include "reaxc_defs.h" #include "pair_reaxc_omp.h" +#include "reaxc_defs.h" #include "reaxc_bond_orders_omp.h" #include "reaxc_bonds_omp.h" @@ -44,6 +43,9 @@ #include "reaxc_valence_angles_omp.h" #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 22d9df7702ca427508b15d2262ac67be36d0afbd..029062470d9109e305e3a223746909360571d317 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -26,10 +26,8 @@ . ----------------------------------------------------------------------*/ -#include "omp_compat.h" #include "reaxc_hydrogen_bonds_omp.h" -#include -#include + #include "fix_omp.h" #include "pair_reaxc_omp.h" #include "reaxc_defs.h" @@ -38,6 +36,9 @@ #include "reaxc_valence_angles_omp.h" // To access Calculate_dCos_ThetaOMP() #include "reaxc_vector.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index b0cf4a5fb8c8fb86be135c183e3e2f666ea603b7..fd216844eb5052b6ae11843638cf968bea3938be 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -27,7 +27,7 @@ ----------------------------------------------------------------------*/ #include "reaxc_init_md_omp.h" -#include + #include "reaxc_defs.h" #include "reaxc_forces.h" #include "reaxc_forces_omp.h" @@ -38,6 +38,8 @@ #include "error.h" #include "fmt/format.h" +#include + // Functions defined in reaxc_init_md.cpp extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); extern int Init_System(reax_system*, control_params*, char*); diff --git a/src/USER-OMP/reaxc_init_md_omp.h b/src/USER-OMP/reaxc_init_md_omp.h index 8416a768cfb767e5c11c60d00b8a2fdb355d0247..45478ec63212a8ce81a6e2070863e9c2c3bf541c 100644 --- a/src/USER-OMP/reaxc_init_md_omp.h +++ b/src/USER-OMP/reaxc_init_md_omp.h @@ -31,6 +31,8 @@ #include "reaxc_types.h" +#include + void InitializeOMP( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); #endif diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index 5f4b6d4eb05f292e666806e5a5a45fccdd656809..57c056fff76bc138ef3afd1c07d422265d8614f9 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -27,14 +27,16 @@ ----------------------------------------------------------------------*/ #include "reaxc_multi_body_omp.h" -#include -#include + #include "fix_omp.h" -#include #include "pair_reaxc_omp.h" + #include "reaxc_defs.h" #include "reaxc_list.h" +#include +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index 564088880ad6bec5d3ad5c4aa3419a76f822cb9f..3c3ca12575d3e75da976bc945baacc38efa622dd 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -27,17 +27,17 @@ ----------------------------------------------------------------------*/ #include "pair_reaxc_omp.h" -#include "thr_data.h" #include "reaxc_defs.h" #include "reaxc_types.h" #include "reaxc_nonbonded.h" #include "reaxc_nonbonded_omp.h" -#include "reaxc_bond_orders_omp.h" #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index 68bacb72027f8717c97fbcc2c3580020edbcbfc4..7d567b259c9fb5c6aaabf13c77574797a4c8f785 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -27,7 +27,7 @@ ----------------------------------------------------------------------*/ #include "reaxc_torsion_angles_omp.h" -#include + #include "fix_omp.h" #include "pair_reaxc_omp.h" @@ -36,6 +36,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 104fadbbae19be5b827f9da14c04731b37f62c7f..f9117d3a5324052d76ebd3593197ac403249b6f1 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -27,11 +27,10 @@ ----------------------------------------------------------------------*/ #include "reaxc_valence_angles_omp.h" -#include -#include -#include "pair_reaxc_omp.h" -#include "fix_omp.h" + #include "error.h" +#include "fix_omp.h" +#include "pair_reaxc_omp.h" #include "reaxc_defs.h" #include "reaxc_types.h" @@ -39,6 +38,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include + #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp index b5e5293aa42dd871ca69252283c3d32e717d651f..b8d0af5c861c386206af9e7a832ac932163c24ff 100644 --- a/src/USER-OMP/respa_omp.cpp +++ b/src/USER-OMP/respa_omp.cpp @@ -15,25 +15,25 @@ Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL) ------------------------------------------------------------------------- */ -#include "omp_compat.h" #include "respa_omp.h" -#include "neighbor.h" -#include "comm.h" + +#include "angle.h" #include "atom.h" -#include "domain.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "update.h" -#include "modify.h" -#include "error.h" -#include "timer.h" +#include "omp_compat.h" #if defined(_OPENMP) #include #endif diff --git a/src/USER-OMP/thr_data.h b/src/USER-OMP/thr_data.h index 4853d6dbbf86177a019eb7984547c7b7c2f15f3a..4b87357101dd506bb6a31b250f6ba2d7d6ce496c 100644 --- a/src/USER-OMP/thr_data.h +++ b/src/USER-OMP/thr_data.h @@ -18,7 +18,7 @@ #ifndef LMP_THR_DATA_H #define LMP_THR_DATA_H -#include "timer.h" +#include "timer.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp index c086f6d6b5dd277d862a1d3cd01297d1f05839fd..6e096defa8f14a6973af789cd505441c417dc5c1 100644 --- a/src/USER-OMP/thr_omp.cpp +++ b/src/USER-OMP/thr_omp.cpp @@ -24,7 +24,7 @@ #include "force.h" #include "modify.h" #include "neighbor.h" -#include "timer.h" + #include "thr_omp.h" diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index adfcf6adb5da228220eb381d9e065449f82a36fd..238aa7c96e05ea7e820c4b29837f20e7e382e8fe 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -2,28 +2,29 @@ // Created by charlie sievers on 6/21/18. // -#include -#include -#include #include "dynamical_matrix.h" + +#include "angle.h" #include "atom.h" -#include "domain.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" #include "error.h" -#include "group.h" +#include "finish.h" #include "force.h" -#include "memory.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "memory.h" #include "modify.h" #include "neighbor.h" #include "pair.h" #include "timer.h" -#include "finish.h" +#include "update.h" + +#include +#include #include using namespace LAMMPS_NS; diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp index 17325b062a42e44ff0fac325e520d078841ca996..382eabe82de7539af3e254fe7ef0a552c03c4388 100644 --- a/src/USER-PHONON/fix_phonon.cpp +++ b/src/USER-PHONON/fix_phonon.cpp @@ -23,7 +23,7 @@ konglt@sjtu.edu.cn; konglt@gmail.com ------------------------------------------------------------------------- */ -#include + #include #include #include "fix_phonon.h" diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index 6e097108332e1afda3f96f1d386f53fa51cbce97..e7997d639727a3d1378dc09edc1753655d27c6b0 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -3,29 +3,28 @@ // #include "third_order.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" -#include "domain.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" #include "error.h" -#include "group.h" +#include "finish.h" #include "force.h" -#include "memory.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "math_special.h" +#include "memory.h" #include "neighbor.h" #include "pair.h" #include "timer.h" -#include "finish.h" -#include "math_special.h" +#include "update.h" + +#include #include -#include using namespace LAMMPS_NS; using namespace MathSpecial; @@ -170,13 +169,11 @@ void ThirdOrder::options(int narg, char **arg) if (narg < 0) error->all(FLERR,"Illegal third_order command"); int iarg = 0; const char *filename = "third_order.dat"; - std::stringstream fss; while (iarg < narg) { if (strcmp(arg[iarg],"file") == 0) { if (iarg+2 > narg) error->all(FLERR, "Illegal third_order command"); - fss << arg[iarg + 1]; - filename = fss.str().c_str(); + filename = arg[iarg + 1]; file_flag = 1; iarg += 2; } else if (strcmp(arg[iarg],"binary") == 0) { diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp index 3a52bbaaa1de2f9dca1a2c102605b5dd8ede3b1d..b7a29c7bc96eda54d8514daa46466ba4f71311a5 100644 --- a/src/USER-PLUMED/fix_plumed.cpp +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "atom.h" @@ -33,7 +33,7 @@ #include "compute.h" #include "modify.h" #include "pair.h" -#include "utils.h" + #include "timer.h" #include "plumed/wrapper/Plumed.h" diff --git a/src/USER-PTM/ptm_deformation_gradient.h b/src/USER-PTM/ptm_deformation_gradient.h index 546efab4376edceb4f150d78319adf5aeecc8ce9..6c686431f66a1ef732a7c3a3b23d3653a86267cb 100644 --- a/src/USER-PTM/ptm_deformation_gradient.h +++ b/src/USER-PTM/ptm_deformation_gradient.h @@ -10,9 +10,11 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI #ifndef PTM_DEFORMATION_GRADIENT_H #define PTM_DEFORMATION_GRADIENT_H -#include #include "ptm_constants.h" +#include +#include + namespace ptm { void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res); diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index f1a34d95380b751e437d052ca13dc25e099856f9..9f07030004c51b757db28a0a1b99b46befe58282 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -15,7 +15,7 @@ Contributing author: Axel Kohlmeyer (ICTP) ------------------------------------------------------------------------- */ -#include + #include #include "fix_qmmm.h" #include "atom.h" diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp index b590e1ae9a6986f989473249020e486a68e0708c..034738023c5fc026875d2d3ea224af27fa0a8b5b 100644 --- a/src/USER-QTB/fix_qbmsst.cpp +++ b/src/USER-QTB/fix_qbmsst.cpp @@ -17,11 +17,11 @@ ------------------------------------------------------------------------- */ #include "fix_qbmsst.h" -#include + #include #include -#include -#include + + #include "atom.h" #include "force.h" #include "update.h" @@ -34,8 +34,8 @@ #include "error.h" #include "kspace.h" #include "math_const.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp index 80c0efddab5de597195a8c5689ddc98a2f13b121..3f29229bebe672fd7b548e4460e723700fe8fd61 100644 --- a/src/USER-QTB/fix_qtb.cpp +++ b/src/USER-QTB/fix_qtb.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_qtb.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "update.h" @@ -32,8 +32,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 64c56cb0e6647ff28999bd5761f60dd08e1132ea..5511efe681fc0ec910ee716f4d593756c0f6d095 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -16,10 +16,10 @@ Aidan Thompson (Sandia, athomps@sandia.gov) ------------------------------------------------------------------------- */ -#include + #include #include -#include + #include #include "pair_quip.h" #include "atom.h" diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 99d016f1a0e0da9365ac8831bce8423f2eb56a70..5d57b740561a12a54d55254dc5439bdfc5fc439d 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -16,36 +16,37 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu) ------------------------------------------------------------------------- */ #include "fix_bond_react.h" -#include -#include -#include -#include -#include "update.h" -#include "modify.h" -#include "respa.h" + #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" +#include "citeme.h" #include "comm.h" #include "domain.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "random_mars.h" -#include "reset_mol_ids.h" -#include "molecule.h" +#include "error.h" +#include "force.h" #include "group.h" -#include "citeme.h" +#include "input.h" #include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "input.h" +#include "modify.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "random_mars.h" +#include "reset_mol_ids.h" +#include "respa.h" +#include "update.h" #include "variable.h" -#include "fmt/format.h" + #include "superpose3d.h" +#include +#include +#include + #include using namespace LAMMPS_NS; diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 433fd82bcd15e078840346d8597285cf36708c78..4a61cfa03bee9ce7773962b28f4a8d96e8ceeec7 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -19,7 +19,7 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_reax.h" -#include + #include #include #include "pair_reaxc.h" diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp index 5c57fed261e6d73f38f7a716b4efdf4ea8c05794..c0ffd4c17e89d23d6c718f1f6ff856716b82aac1 100644 --- a/src/USER-REAXC/fix_reaxc_bonds.cpp +++ b/src/USER-REAXC/fix_reaxc_bonds.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_bonds.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp index 74692f1c9b6f0d291664a58f7096db8544e4f2d4..ec03ab18081177eee91531f39a06f6617dd693a6 100644 --- a/src/USER-REAXC/fix_reaxc_species.cpp +++ b/src/USER-REAXC/fix_reaxc_species.cpp @@ -17,8 +17,8 @@ ------------------------------------------------------------------------- */ #include "fix_reaxc_species.h" -#include -#include + + #include #include "fix_ave_atom.h" #include "atom.h" diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index e0888e8514bbfd72982e50096e5049c95d60650e..c38257ae30590ef433086e4b2b208e73891b7c28 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -21,9 +21,9 @@ ------------------------------------------------------------------------- */ #include "pair_reaxc.h" -#include + #include -#include + #include #include #include "atom.h" @@ -39,7 +39,7 @@ #include "citeme.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "reaxc_defs.h" #include "reaxc_types.h" diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp index b215e8d278f9c3892e99fce85405fb84b6a504c7..bf2fc73b015c97ea1506a56c59d80f8fc4f6593c 100644 --- a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -19,18 +19,19 @@ ------------------------------------------------------------------------- */ #include "pair_sdpd_taitwater_isothermal.h" -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include "update.h" -#include "utils.h" + +#include + #ifndef USE_ZEST #include "random_mars.h" #endif diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp index 670783a3d7dfe8c462418523478f204c79f5ac79..81a43ff7f3543276dd5ba6a1f692348233cd8ae2 100644 --- a/src/USER-SMD/atom_vec_smd.cpp +++ b/src/USER-SMD/atom_vec_smd.cpp @@ -23,9 +23,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_smd.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp index 09aeeea74aa65d755be7a69c69d7cf88b86829d2..81792355e013d44c8eae8b1df9d9d8ae0e976d06 100644 --- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp +++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp @@ -23,14 +23,16 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_defgrad.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp index ba1a9306ef6ba4401a0e58cd80365ff2140cd9be..a3727871de02ff3a62bca6f04e9ebc55bb6f32b2 100644 --- a/src/USER-SMD/compute_smd_tlsph_shape.cpp +++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp @@ -23,16 +23,18 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_shape.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp index f0061bf7a1cbd699ef8c91f67b8620963d648870..db51ca412539a4eb2540ae7990281bedcab84bbe 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp @@ -24,16 +24,18 @@ ------------------------------------------------------------------------- */ #include "compute_smd_tlsph_strain.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace std; diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp index 895a973f6a1863c4faacbe59aa33d8fd18044211..577dc0e40f66b326214d6ee4528daf4697e59a60 100644 --- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp +++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp @@ -23,17 +23,19 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include -#include #include "compute_smd_tlsph_strain_rate.h" + #include "atom.h" -#include "update.h" -#include "modify.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "modify.h" #include "pair.h" +#include "update.h" + +#include +#include // IWYU pragma: export using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp index eb1f144275406effe900d1cef15d645b969d0d33..5999dfaa5df0c4a842ecdf538abb7cf221019bae 100644 --- a/src/USER-SMD/compute_smd_vol.cpp +++ b/src/USER-SMD/compute_smd_vol.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include "compute_smd_vol.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp index ab6dd5ef5c50b5c97c5eb552b305ae6a34c3df57..b5dab3d3a15d6eca99d13e975cecfbf4b31068b1 100644 --- a/src/USER-SMD/fix_smd_adjust_dt.cpp +++ b/src/USER-SMD/fix_smd_adjust_dt.cpp @@ -23,8 +23,8 @@ ------------------------------------------------------------------------- */ #include "fix_smd_adjust_dt.h" -#include -#include + + #include "update.h" #include "force.h" #include "pair.h" diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp index 2aa6f980ed8c2b2c8c1c2517d70fd31872c8abb5..e0e76a18fbd096db791d95ac634e8577d0e7fb92 100644 --- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp +++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp @@ -23,15 +23,16 @@ ------------------------------------------------------------------------- */ #include "fix_smd_move_triangulated_surface.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "update.h" #include "error.h" #include "math_const.h" +#include "update.h" + +#include +#include +#include using namespace Eigen; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp index 895e5b1a25dffca7cbbd7e4e45b872ca4b8e579e..d3e71f0e50e92bd6140498360f7893b1857a5dba 100644 --- a/src/USER-SMD/fix_smd_setvel.cpp +++ b/src/USER-SMD/fix_smd_setvel.cpp @@ -24,18 +24,18 @@ ------------------------------------------------------------------------- */ #include "fix_smd_setvel.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "region.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp index 4ade21a6fdf3b9e169e6f1ea8ab3ded286130b26..3e63de08f3a08317147c010c80adc95e36c1cf17 100644 --- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp +++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp @@ -25,7 +25,7 @@ ------------------------------------------------------------------------- */ #include "fix_smd_tlsph_reference_configuration.h" -#include + #include #include "atom.h" #include "comm.h" diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp index ba3a324d5698a5b7332c5018015d1f3c207c3bbf..10f248c39fe4332b78786d5ce3ed918a5e489b72 100644 --- a/src/USER-SMD/fix_smd_wall_surface.cpp +++ b/src/USER-SMD/fix_smd_wall_surface.cpp @@ -16,17 +16,16 @@ ------------------------------------------------------------------------- */ #include "fix_smd_wall_surface.h" -#include -#include -#include -#include + #include "atom.h" -#include "domain.h" -#include "force.h" +#include "atom_vec.h" #include "comm.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "atom_vec.h" +#include "memory.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 67fda5f18d8b171da6dff50451546222acfd3720..8d3c06d5e6d3519d17a9ae4ebbda4514b61b20f2 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -27,9 +27,9 @@ ------------------------------------------------------------------------- */ #include "pair_smd_hertz.h" -#include + #include -#include + #include #include "atom.h" #include "domain.h" @@ -40,7 +40,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index 1ba4b37520067e3e87dc9f60f36069abb2140a90..25301685a7376ddefc0f5ff88a80d9f50bcd9197 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -23,10 +23,10 @@ ------------------------------------------------------------------------- */ #include "pair_smd_tlsph.h" -#include + #include #include -#include + #include #include #include "fix_smd_tlsph_reference_configuration.h" diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index 92438837193ec47cbe06ed734e6099145a5f3b37..8ccba562e26f4cdda6bdffa8a3f5e368947c155c 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -27,9 +27,9 @@ ------------------------------------------------------------------------- */ #include "pair_smd_triangulated_surface.h" -#include + #include -#include + #include #include #include "atom.h" @@ -41,7 +41,7 @@ #include "neigh_request.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace std; using namespace LAMMPS_NS; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index ecd0d5f4ec31bf25164e54a43442232c3575f73f..3a6cdf5d2f16672aa73d4d94a8dfc6ce9dbe12d6 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -23,24 +23,22 @@ ------------------------------------------------------------------------- */ #include "pair_smd_ulsph.h" -#include -#include -#include -#include -#include + #include "atom.h" -#include "domain.h" -#include "force.h" -#include "update.h" #include "comm.h" -#include "neighbor.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include "smd_kernels.h" #include "smd_material_models.h" #include "smd_math.h" -#include "smd_kernels.h" +#include "update.h" + +#include +#include using namespace SMD_Kernels; using namespace std; diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp index 096600df5207a003a57607cc0174c85aa3cfb368..942b6a8cabd941167f7ae692ffe09806e1ee084f 100644 --- a/src/USER-SMD/smd_material_models.cpp +++ b/src/USER-SMD/smd_material_models.cpp @@ -22,12 +22,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "smd_material_models.h" + +#include "math_special.h" + #include #include -#include #include #include -#include "math_special.h" #include diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index f6ecd40bb65912e20d22f227098050692da89778..875d254ac9b1a143a3588594cb319d2a827b448a 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -39,9 +39,9 @@ ------------------------------------------------------------------------- */ #include "pair_smtbq.h" -#include + #include -#include + #include #include #include diff --git a/src/USER-SPH/atom_vec_sph.cpp b/src/USER-SPH/atom_vec_sph.cpp index 2811c57e6c25c0b97cd9c3fae6464fb8e336ea01..93ca2b60a7792a4bfab3d7a85ac97ca1199d997b 100644 --- a/src/USER-SPH/atom_vec_sph.cpp +++ b/src/USER-SPH/atom_vec_sph.cpp @@ -12,9 +12,10 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sph.h" -#include + #include "atom.h" -#include "error.h" + +#include using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 7bb06c14d960a1f6cadc83fe0aedb4b154768590..fb8c928f2dd36b1630d1a24bc0e1d81424db74e2 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -19,7 +19,7 @@ #include "error.h" #include "neigh_list.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index c80e2b4725a203ed518b591d288ab02e3fb8e508..5480ff8e4c7d1f1031bc9c68661e06e418f90115 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -19,7 +19,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index 4004e415745b7d1423dcc69abb2ada5b08571b0e..eb76d800c8dd5ef00c12c9ab106e9cfa1ddc9fb3 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -19,7 +19,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index c70cc7cd8366cd899267934d2c7059f84d13a8dd..3d3065f839a53a90a2b04c6f98eddbeb8093f796 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "pair_sph_rhosum.h" + #include "atom.h" -#include "force.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" #include "neighbor.h" #include "update.h" -#include "domain.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index 6455c1e8be4c1243a01d51be4da1f0f8c671012b..c0051201d0ebb3d6f6ce45d9ccb8363ecfb395c0 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -20,7 +20,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 7a6188da69349a6bf1c98e8467448ac6c0a6140a..497aea293b9b23c8ca7f9e44ed048f32c42404dc 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -20,7 +20,7 @@ #include "memory.h" #include "error.h" #include "domain.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp index 9d15fbc44139c50cf456bb1e5a9f1302916447cd..d010b004d501f2642098f94ccd501271c2a90c08 100644 --- a/src/USER-TALLY/compute_force_tally.cpp +++ b/src/USER-TALLY/compute_force_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_force_tally.h" -#include + #include #include "atom.h" #include "group.h" diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp index 350bc4b4b6b75989218ef23b83dc4b3a5b33ebe2..1a2dd36285418fdf7d69081ddb042ea94b8aa2df 100644 --- a/src/USER-TALLY/compute_heat_flux_tally.cpp +++ b/src/USER-TALLY/compute_heat_flux_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_heat_flux_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp index ce647a04c3fc966f003e945973dbd8cc03de26da..835d1e80bdac811407246bf8dcaea81b27830058 100644 --- a/src/USER-TALLY/compute_pe_mol_tally.cpp +++ b/src/USER-TALLY/compute_pe_mol_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe_mol_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp index edfa49b1b1e2a6857e950614ed9f1bb415d4fae0..ef7c13fed212e3a6d3e98276c528f8e3a918639f 100644 --- a/src/USER-TALLY/compute_pe_tally.cpp +++ b/src/USER-TALLY/compute_pe_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp index 1ea096e2865592a0cc46fdef0bf72d73e9c6a968..2a0cbc8e4bf058f26dc50e89f70f2b6bdae9c742 100644 --- a/src/USER-TALLY/compute_stress_tally.cpp +++ b/src/USER-TALLY/compute_stress_tally.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_stress_tally.h" -#include + #include "atom.h" #include "group.h" #include "pair.h" diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index 72ed2640d8723fd425716596d670706d398c96cc..59dba0d90d679336f78e88bc3862c2b8fbb1a121 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -23,7 +23,7 @@ ------------------------------------------------------------------------- */ #include -#include + #include #include "dump_vtk.h" #include "atom.h" diff --git a/src/USER-VTK/dump_vtk.h b/src/USER-VTK/dump_vtk.h index e8de87f11cab52e998258bbc59d38cf46dc27bd3..b9db1f88cbb3845c1706e70be6890947dec2d30d 100644 --- a/src/USER-VTK/dump_vtk.h +++ b/src/USER-VTK/dump_vtk.h @@ -27,7 +27,7 @@ DumpStyle(vtk,DumpVTK) #include "dump_custom.h" #include #include -#include + #include #include diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp index 9c925d2365c6dcf96dc1c6bbcbc0a6232c5f72f5..c45af1d1985d6d62dd9c7d39157846f85a6be0db 100644 --- a/src/USER-YAFF/angle_cross.cpp +++ b/src/USER-YAFF/angle_cross.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_cross.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp index 38a2cea3aaaf3c5a90293b63d68dca709ae4ef7f..34de7726724fe1e304921fd00ab584f8a300827e 100644 --- a/src/USER-YAFF/angle_mm3.cpp +++ b/src/USER-YAFF/angle_mm3.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "angle_mm3.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp index 39f238f1abbac0ba1e173e18adf3e5d06517712e..f5d5fed946fb058c1f85f2634c66a9f0f5b4fc37 100644 --- a/src/USER-YAFF/bond_mm3.cpp +++ b/src/USER-YAFF/bond_mm3.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "bond_mm3.h" -#include + #include #include "atom.h" #include "neighbor.h" @@ -24,7 +24,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp index e9b454bdb932e1c55c2afbffe58bc0f43d16ccda..37039b27e4acac02eee7b16a501b4fc2b44a374d 100644 --- a/src/USER-YAFF/improper_distharm.cpp +++ b/src/USER-YAFF/improper_distharm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_distharm.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp index af5086917a52908bb5401be1938af304b8abe1a6..ddc4d78c93a0ebdc03b4d9d77f8c0d6f649e8027 100644 --- a/src/USER-YAFF/improper_sqdistharm.cpp +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "improper_sqdistharm.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp index 2cbf01f7b7bc093c6b58b0da6cf77e3e5f685d0d..98fd317794ea0a336147b9f6f9ca4dcc0e55cc61 100644 --- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_switch3_coulgauss_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp index 52bcf20b9b8d4f1c1c0f6975d67f11bca0914863..e1ee0e0b98ae7c6921b67fa3aff10bd313c258b2 100644 --- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_mm3_switch3_coulgauss_long.h" -#include + #include #include #include "atom.h" @@ -31,7 +31,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index bda4299a68108cbced26e9f40ba02779bbe71584..be77b8457b8c94d9621726be368a2add2b5087ce 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_voronoi_atom.h" -#include + #include #include #include diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index fb3f90ec28bf8874886eed5562cd811737968bf8..7c2426739d99d3bbd145375ed73b26760bb1ac00 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -16,12 +16,10 @@ ------------------------------------------------------------------------- */ #include "angle_deprecated.h" -#include #include "angle_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index d0a1d29e652f2fe4d4f938477842ca46d1bde2cf..56590d6757da47fef17466fe84992722d973ee84 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "angle_hybrid.h" -#include -#include -#include + #include "atom.h" #include "neighbor.h" #include "comm.h" #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index eb9cbf1ea2796bf5bfe81cabc64f6a9ba973fd00..e087b774e0c2aab68edbc50ad5645c6478020e01 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -16,15 +16,14 @@ ------------------------------------------------------------------------- */ #include "angle_zero.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom.cpp b/src/atom.cpp index f4c93db4593eefe972fc741959381f4ff8fdf286..90dce44764cf377693a50a751c9a6ba7755054a5 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -12,31 +12,27 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include -#include -#include -#include -#include -#include -#include "style_atom.h" #include "atom_vec.h" -#include "atom_vec_ellipsoid.h" +#include "style_atom.h" // IWYU pragma: keep + #include "comm.h" -#include "neighbor.h" -#include "force.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "update.h" #include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "group.h" #include "input.h" -#include "variable.h" -#include "molecule.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "molecule.h" +#include "neighbor.h" +#include "update.h" +#include "variable.h" + +#include +#include #ifdef LMP_USER_INTEL #include "neigh_request.h" diff --git a/src/atom.h b/src/atom.h index 4dac15d758ec9adb2b91004cb9c7cc342c2cb18f..21b9c06f8c1729a16b6867bc5eb8bd3d5f05b85d 100644 --- a/src/atom.h +++ b/src/atom.h @@ -15,16 +15,20 @@ #define LMP_ATOM_H #include "pointers.h" + #include #include -#include namespace LAMMPS_NS { + // forward declaration + + class AtomVec; + class Atom : protected Pointers { public: char *atom_style; - class AtomVec *avec; + AtomVec *avec; enum{DOUBLE,INT,BIGINT}; // atom counts @@ -273,12 +277,12 @@ class Atom : protected Pointers { void add_peratom_vary(const char *, void *, int, int *, void *, int collength=0); void create_avec(const std::string &, int, char **, int); - virtual class AtomVec *new_avec(const std::string &, int, int &); + virtual AtomVec *new_avec(const std::string &, int, int &); void init(); void setup(); - class AtomVec *style_match(const char *); + AtomVec *style_match(const char *); void modify_params(int, char **); void tag_check(); void tag_extend(); @@ -296,8 +300,8 @@ class Atom : protected Pointers { void data_angles(int, char *, int *, tagint, int); void data_dihedrals(int, char *, int *, tagint, int); void data_impropers(int, char *, int *, tagint, int); - void data_bonus(int, char *, class AtomVec *, tagint); - void data_bodies(int, char *, class AtomVec *, tagint); + void data_bonus(int, char *, AtomVec *, tagint); + void data_bodies(int, char *, AtomVec *, tagint); void data_fix_compute_variable(int, int); virtual void allocate_type_arrays(); diff --git a/src/atom_map.cpp b/src/atom_map.cpp index c23aeec83cd442186e71a1acdffc75d5de756943..02b97a1134e43f25224575d45e21c206c77324ab 100644 --- a/src/atom_map.cpp +++ b/src/atom_map.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "atom.h" -#include -#include + #include "comm.h" -#include "memory.h" #include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp index 261b06899714f6e5ff4a4d299a9b28e569bb392b..4a00e5852b829a54cd096d97cca994cc8293caf5 100644 --- a/src/atom_vec.cpp +++ b/src/atom_vec.cpp @@ -12,20 +12,19 @@ ------------------------------------------------------------------------- */ #include "atom_vec.h" -#include -#include + #include "atom.h" #include "comm.h" #include "domain.h" -#include "force.h" -#include "modify.h" +#include "error.h" #include "fix.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" #include "tokenizer.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 10cbb9c84131c676add5d13c31d232500a46457f..608c803e203e5a2c7d397228f40f79e51f297fc5 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "atom_vec_body.h" -#include -#include -#include "my_pool_chunk.h" -#include "style_body.h" -#include "body.h" +#include "style_body.h" // IWYU pragma: keep + #include "atom.h" -#include "domain.h" -#include "modify.h" +#include "body.h" +#include "error.h" #include "fix.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "my_pool_chunk.h" + +#include using namespace LAMMPS_NS; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index dc2760c5f91adbfee47d4f2a1ee2189337732499..c22111f48cecc7173a241a59f59493d070efb8c7 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "atom_vec_ellipsoid.h" -#include -#include "math_extra.h" + #include "atom.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp index db593dcee0df239d3357c417f385dd91b3046fa3..7a8c73570d02fbe17fed05cca56c646d565d25ad 100644 --- a/src/atom_vec_hybrid.cpp +++ b/src/atom_vec_hybrid.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "atom_vec_hybrid.h" -#include + #include "atom.h" #include "comm.h" -#include "memory.h" #include "error.h" #include "tokenizer.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; @@ -595,7 +595,7 @@ void AtomVecHybrid::build_styles() nallstyles = 0; #define ATOM_CLASS #define AtomStyle(key,Class) nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS @@ -609,7 +609,7 @@ void AtomVecHybrid::build_styles() allstyles[nallstyles] = new char[n]; \ strcpy(allstyles[nallstyles],#key); \ nallstyles++; -#include "style_atom.h" +#include "style_atom.h" // IWYU pragma: keep #undef AtomStyle #undef ATOM_CLASS } diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index af768f99431c4bcae5b9026b71fa42660bc7b5a9..88dcb8c2fa8d185f341e51872a015056802520ea 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "atom_vec_line.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp index 03f417b1d03042db40f5b3a40588133f5e1ad1dd..03412a11ccfb567188462b7d4462e16b1ccb3765 100644 --- a/src/atom_vec_sphere.cpp +++ b/src/atom_vec_sphere.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "atom_vec_sphere.h" -#include + #include "atom.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_adapt.h" #include "math_const.h" -#include "error.h" -#include "utils.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index d5b48b95401e83a08d0a103866f18bcfacfd1693..e391a73215401263fa8b90a5ab412c5f64d4cccd 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -12,18 +12,18 @@ ------------------------------------------------------------------------- */ #include "atom_vec_tri.h" -#include -#include -#include "math_extra.h" + #include "atom.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/balance.cpp b/src/balance.cpp index 168d7f59a4d5362cbd2e58dd35dc4235b87a52ee..af8d9048129a0afaa669ca5d6ec114a37b507dde 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -19,28 +19,26 @@ // #define BALANCE_DEBUG 1 #include "balance.h" -#include -#include -#include + #include "atom.h" #include "comm.h" -#include "rcb.h" -#include "irregular.h" #include "domain.h" -#include "force.h" -#include "update.h" -#include "modify.h" +#include "error.h" #include "fix_store.h" #include "imbalance.h" #include "imbalance_group.h" -#include "imbalance_time.h" #include "imbalance_neigh.h" #include "imbalance_store.h" +#include "imbalance_time.h" #include "imbalance_var.h" +#include "irregular.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "rcb.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/body.h b/src/body.h index 1c742d3e65d029df19af8d1e8f1590db6a775e98..c9c289792e5b896b0c0cbe2ec797b70b12eb800e 100644 --- a/src/body.h +++ b/src/body.h @@ -15,7 +15,7 @@ #define LMP_BODY_H #include "pointers.h" -#include "atom_vec_body.h" +#include "atom_vec_body.h" // IWYU pragma: keep namespace LAMMPS_NS { diff --git a/src/bond.cpp b/src/bond.cpp index 12659fd8aa26b5c2eaf761b4f8c89d535beb1ab3..1f953bbd1904c007ccc378d26478ef37e8ca14a8 100644 --- a/src/bond.cpp +++ b/src/bond.cpp @@ -12,20 +12,18 @@ ------------------------------------------------------------------------- */ #include "bond.h" -#include -#include -#include + #include "atom.h" +#include "atom_masks.h" #include "comm.h" +#include "error.h" #include "force.h" +#include "memory.h" #include "neighbor.h" #include "suffix.h" -#include "atom_masks.h" -#include "memory.h" -#include "error.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index 0d91f73ea76d9e2a8ff0899b3ca791c0021680de..5422ab35f6b30cd764409c3c876446732b434650 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -16,12 +16,11 @@ ------------------------------------------------------------------------- */ #include "bond_deprecated.h" -#include + #include "bond_hybrid.h" #include "comm.h" -#include "force.h" #include "error.h" -#include "utils.h" +#include "force.h" using namespace LAMMPS_NS; diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index 2fe9f7d3887b40cbf5c6ad0744332f9e673624b4..b42683c3005655335b0e3f9e088e11c7f96ae897 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "bond_hybrid.h" -#include -#include -#include + #include "atom.h" -#include "neighbor.h" #include "comm.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 8053c5531de7c071a995d42d5424d311186ce559..71146ec4d66a6bc770c8a9e8ae48027a3fc439d1 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "bond_zero.h" -#include -#include + #include "atom.h" -#include "force.h" #include "comm.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/change_box.cpp b/src/change_box.cpp index 5fe4eb8a06f57e59dc29758c69fc9ceab5acc895..1bd3fe733f948afc51039bdd15bbf911a9f43c4b 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -12,22 +12,20 @@ ------------------------------------------------------------------------- */ #include "change_box.h" -#include -#include -#include + #include "atom.h" -#include "modify.h" -#include "fix.h" -#include "domain.h" -#include "lattice.h" #include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "group.h" #include "irregular.h" +#include "lattice.h" +#include "modify.h" #include "output.h" -#include "group.h" -#include "error.h" -#include "force.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/comm.cpp b/src/comm.cpp index 7e603f21049446b8b4ce0bccdd41024540dc7504..7b351e12fc384bd184fcd4b9fd93179b4c1fcbcf 100644 --- a/src/comm.cpp +++ b/src/comm.cpp @@ -12,31 +12,29 @@ ------------------------------------------------------------------------- */ #include "comm.h" -#include -#include -#include -#include "universe.h" -#include "atom.h" + +#include "accelerator_kokkos.h" +#include "atom.h" // IWYU pragma: keep #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "modify.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" -#include "domain.h" -#include "output.h" +#include "domain.h" // IWYU pragma: keep #include "dump.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "group.h" -#include "procmap.h" #include "irregular.h" -#include "accelerator_kokkos.h" -#include "memory.h" -#include "error.h" +#include "memory.h" // IWYU pragma: keep +#include "modify.h" +#include "neighbor.h" // IWYU pragma: keep +#include "output.h" +#include "pair.h" +#include "procmap.h" +#include "universe.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include #ifdef _OPENMP #include diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index c5ec8b35f4e353230b7788b7163ed6e6a8eec155..37a4f0ae3d3134897fab2be27f515cf0180fdba7 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -16,19 +16,20 @@ ------------------------------------------------------------------------- */ #include "comm_brick.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "pair.h" -#include "domain.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" #include "error.h" +#include "fix.h" #include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp index 9f0169568d27eba241ebb1bed5aac9a9905d129b..48c9680d2fa22d4b8f4fdb5f65155ca6978dfd9c 100644 --- a/src/comm_tiled.cpp +++ b/src/comm_tiled.cpp @@ -17,19 +17,20 @@ ------------------------------------------------------------------------- */ #include "comm_tiled.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" -#include "pair.h" -#include "neighbor.h" -#include "fix.h" #include "compute.h" +#include "domain.h" #include "dump.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "memory.h" +#include "neighbor.h" +#include "pair.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute.cpp b/src/compute.cpp index 208b93730ee11cb0a474797315c07222f24d6ece..4cde9ff567ea8dc4a7920ce4e45c2a2fba5b48c9 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -12,16 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute.h" -#include -#include + +#include "atom_masks.h" #include "domain.h" -#include "force.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "atom_masks.h" +#include "group.h" #include "memory.h" -#include "error.h" +#include "modify.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index 0bd329079a807158ee2029bfee8af993560b0eb8..5d55f1fbbb0eecf974a658dd754b842996478aeb 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "compute_adf.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "comm.h" -#include "utils.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp index 6e28a94388b05f835584b3e4f7d8421c802fc9b7..6b6f376b4c5422aab406b6e65a6ce9e58985d137 100644 --- a/src/compute_aggregate_atom.cpp +++ b/src/compute_aggregate_atom.cpp @@ -16,23 +16,23 @@ ------------------------------------------------------------------------- */ #include "compute_aggregate_atom.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "pair.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "update.h" -#include "group.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp index fc72a584531d28126881f253d95b09fbdda521b3..e3e44efbbb71f911228b8e6c20721e065bfc1583 100644 --- a/src/compute_angle.cpp +++ b/src/compute_angle.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_angle.h" -#include + #include "angle.h" -#include "update.h" -#include "force.h" #include "angle_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp index 05ea963b82515ce0454a864e28b7a6541117eb2f..6c9f1d65a20ed4cb34774ac7c97ddf3c0abf6675 100644 --- a/src/compute_angmom_chunk.cpp +++ b/src/compute_angmom_chunk.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_angmom_chunk.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp index 5cc947c7646cb0523659d7176a3b0374fed3474b..503582bc65190b896bdd44a041284cedaf7cc3f5 100644 --- a/src/compute_bond.cpp +++ b/src/compute_bond.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_bond.h" -#include + #include "bond.h" -#include "update.h" -#include "force.h" #include "bond_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index ae041c199751be1528ebc05cc45813142d3a9ba7..d0044410d870c6a6a6d1cc32e1466e0d33aabb81 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -14,29 +14,27 @@ // NOTE: allow for bin center to be variables for sphere/cylinder #include "compute_chunk_atom.h" -#include -#include -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "force.h" +#include "comm.h" #include "domain.h" -#include "region.h" -#include "lattice.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "fix_store.h" -#include "comm.h" #include "group.h" #include "input.h" -#include "variable.h" +#include "lattice.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index 579b194b9f526820bb72eb3ebcc1b0ce61d6c4dd..953ae3a8cbfdefcd7d33a98a49652797b8c80f31 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute_chunk_spread_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" -#include "fix.h" #include "compute.h" #include "compute_chunk_atom.h" -#include "input.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp index 021665a647284af3c5d855ed951bbd799442ff64..8086ef3f41aee0272a8544d1fd880dee1d394e61 100644 --- a/src/compute_cluster_atom.cpp +++ b/src/compute_cluster_atom.cpp @@ -12,22 +12,22 @@ ------------------------------------------------------------------------- */ #include "compute_cluster_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "update.h" -#include "group.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp index 8bbe2c15d053c05632f4b8e73a309cbd577725a2..e9b6f1699057db5b809d834f9851ff61fd860a57 100644 --- a/src/compute_cna_atom.cpp +++ b/src/compute_cna_atom.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "compute_cna_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "pair.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp index c39911214c02d1e846156d1864bea1b33c625789..8398311a05de721fe2fbc7dd975d140b185e969f 100644 --- a/src/compute_com_chunk.cpp +++ b/src/compute_com_chunk.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_com_chunk.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp index be2f9c39bd03d28e8f1a54ba8255fcda9f61e810..cb919d3a836783317f19b4b9e231c770e732de19 100644 --- a/src/compute_coord_atom.cpp +++ b/src/compute_coord_atom.cpp @@ -12,22 +12,23 @@ ------------------------------------------------------------------------- */ #include "compute_coord_atom.h" -#include -#include -#include "compute_orientorder_atom.h" + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "compute_orientorder_atom.h" +#include "error.h" +#include "force.h" +#include "group.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "group.h" -#include "memory.h" -#include "error.h" -#include "utils.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_deprecated.cpp b/src/compute_deprecated.cpp index 2419e5bc8be6a19134f15f87684e908399f93cb1..4b7e3dae3cf2ac48426065eea819c2aee0edbd2b 100644 --- a/src/compute_deprecated.cpp +++ b/src/compute_deprecated.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp index e50903104ab49b9b8dae84961acfc188040f5dce..8853887f184a8f825593568e9e70e7c7586576bd 100644 --- a/src/compute_dihedral.cpp +++ b/src/compute_dihedral.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "compute_dihedral.h" -#include -#include "update.h" -#include "force.h" + #include "dihedral.h" #include "dihedral_hybrid.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp index 3790da2035216bf555931af0c4e740f2311f8472..361ee36c1827f59fde2186bd4c2d4b65ecbe6ce3 100644 --- a/src/compute_dipole_chunk.cpp +++ b/src/compute_dipole_chunk.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "compute_dipole_chunk.h" -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "domain.h" -#include "memory.h" #include "error.h" #include "math_special.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index b20dd3bec3b727939d2fd6d096b71320d05e2c8f..4b194cfab128cd2d951e9333614027a52c454e36 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -12,19 +12,20 @@ ------------------------------------------------------------------------- */ #include "compute_displace_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "group.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix_store.h" +#include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_erotate_sphere.cpp b/src/compute_erotate_sphere.cpp index 2a8588f06176ae985cc4b61e070c851cd0e2ff2a..447b28b51a3175cd8b74f3e1dfa3e0a96f98cafa 100644 --- a/src/compute_erotate_sphere.cpp +++ b/src/compute_erotate_sphere.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "compute_erotate_sphere.h" -#include + #include "atom.h" -#include "update.h" -#include "force.h" #include "error.h" +#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp index 664e2fa9ecc5dae860fc148edc64cde40a8c457a..db003c93e7ae63a1a96cd86cd5d2e49c7ba8c809 100644 --- a/src/compute_fragment_atom.cpp +++ b/src/compute_fragment_atom.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "compute_fragment_atom.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "modify.h" -#include "force.h" -#include "group.h" #include "comm.h" -#include "memory.h" #include "error.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp index 0c0e34fa0c12a836f35835001c848b51221fb94c..b3e4f88bf3594aed1a204c6625629a15a7007b36 100644 --- a/src/compute_global_atom.cpp +++ b/src/compute_global_atom.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "compute_global_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index c8876daeef26123db50a46b4209feb42b1fb97db..ca0483fce938245eeb821b48f3f5c31e0c96f60c 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_group_group.h" -#include + #include #include #include "atom.h" diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp index bce0c0de85fff660f24daf5947e21f89a8bf9076..81876109c474f8d36d25acb83f24f42b8f75aadb 100644 --- a/src/compute_gyration.cpp +++ b/src/compute_gyration.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_gyration.h" -#include + #include "update.h" #include "atom.h" #include "group.h" diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp index 5677ce4b6a37f4f17bbd16df1a4317930307593f..ad0520bc01775ce3a5ab0daf2caeafe72d1bb686 100644 --- a/src/compute_gyration_chunk.cpp +++ b/src/compute_gyration_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_gyration_chunk.h" -#include + #include #include #include "atom.h" diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp index 7b607bd4db0f27d22175db0428ab8da1514077eb..15a17949eb6bc879300a95d0efbf725e93a83324 100644 --- a/src/compute_heat_flux.cpp +++ b/src/compute_heat_flux.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "compute_heat_flux.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp index 181771dcfb75f5d064f6e0d9babab24c65979f50..3721dbfd4821f94bd3bbc1d9c82ae2776290881c 100644 --- a/src/compute_improper.cpp +++ b/src/compute_improper.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_improper.h" -#include + #include "update.h" #include "force.h" #include "improper.h" diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp index be980a08ee3c2fbf817d24842b96b69cf7ff2f35..65de1d7bb53fee9579ac516960cf37c8e74b475e 100644 --- a/src/compute_inertia_chunk.cpp +++ b/src/compute_inertia_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_inertia_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_ke.cpp b/src/compute_ke.cpp index c6ba478dcb4568d019f8a4127f61c89a7a053ab3..e673f7fe53a60095d40f1ed21696545cff69439a 100644 --- a/src/compute_ke.cpp +++ b/src/compute_ke.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_ke.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 930f979bf0351b79de771d970e9dfe1db657098b..d23c389ab6f70a3ee95cade68d696134489608dc 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_msd.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "group.h" @@ -22,7 +22,7 @@ #include "modify.h" #include "fix_store.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp index dda921ef42bc99c3704abe3c0c1db7bdd9539a02..b0e2520f997e135398f3cf6fb512795287da2468 100644 --- a/src/compute_msd_chunk.cpp +++ b/src/compute_msd_chunk.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_msd_chunk.h" -#include + #include -#include + #include "atom.h" #include "group.h" #include "update.h" @@ -24,7 +24,7 @@ #include "fix_store.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp index 327c64493fe041cc960bd5ddb1f77fd1ca09e8f1..4151b2cdb8ec2ce55e886b93d78df2b9a5fcafc8 100644 --- a/src/compute_omega_chunk.cpp +++ b/src/compute_omega_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_omega_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp index ade9f7615ede6fc5ed9affca897812e21d60d145..7323b6ef0122dfda227b5f33f1c9dd580838c85e 100644 --- a/src/compute_orientorder_atom.cpp +++ b/src/compute_orientorder_atom.cpp @@ -17,26 +17,25 @@ ------------------------------------------------------------------------- */ #include "compute_orientorder_atom.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" +#include "neighbor.h" #include "pair.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; -using namespace std; #ifdef DBL_EPSILON #define MY_EPSILON (10.0*DBL_EPSILON) diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp index 054a50bed4eb3746956ae7c5866bf293cccd17a4..7ace5615a782ed9c53a02e32abc99b2952f762c4 100644 --- a/src/compute_pair.cpp +++ b/src/compute_pair.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pair.h" -#include + #include #include #include "update.h" diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp index 2018d929f345709806c8eee356aa62e4ebce7e36..e41221f70bae072807b77088434d247886897b5e 100644 --- a/src/compute_pair_local.cpp +++ b/src/compute_pair_local.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "compute_pair_local.h" -#include -#include -#include + #include "atom.h" -#include "update.h" +#include "error.h" #include "force.h" -#include "pair.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp index 379de0f9de3a4655584f67a1a7da8b0abef50c2b..d9ed312328e36db670c18c7e2ed3db90d0ba84ef 100644 --- a/src/compute_pe.cpp +++ b/src/compute_pe.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_pe.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp index 4712c834617682698a8860d615bfd4ba3175b1f3..90e4f9b39c36b2958c3ba580d4b5bdb02edcffe6 100644 --- a/src/compute_pressure.cpp +++ b/src/compute_pressure.cpp @@ -12,23 +12,24 @@ ------------------------------------------------------------------------- */ #include "compute_pressure.h" -#include -#include + +#include "angle.h" #include "atom.h" -#include "update.h" +#include "bond.h" +#include "dihedral.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "error.h" +#include "modify.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp index 579c7cae3fa85e7c458145b66deed9bf01d4b74b..c27cfc4096fa3c8a0a8a8745d53638d570beed43 100644 --- a/src/compute_property_chunk.cpp +++ b/src/compute_property_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_property_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 920228e0563b905a36ee75ad0d94946e9e83ae1e..a28223b3a7cbe5e3978d5cfa43bb1049b5bbb38b 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_rdf.h" -#include + #include #include #include "atom.h" @@ -32,7 +32,7 @@ #include "memory.h" #include "error.h" #include "comm.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index d4730c1de03bde0e5f30e26d0b227bf7e7c0df6a..b024b4365ca0a995dcded0e463e440a140930e25 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_reduce.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "domain.h" @@ -25,7 +25,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/compute_reduce.h b/src/compute_reduce.h index 9701f0e61efa48b0cd04c4c5e75c20e8043391ff..00c1a9a6b90d24d0b50583df385d812db8e151ac 100644 --- a/src/compute_reduce.h +++ b/src/compute_reduce.h @@ -20,7 +20,7 @@ ComputeStyle(reduce,ComputeReduce) #ifndef LMP_COMPUTE_REDUCE_H #define LMP_COMPUTE_REDUCE_H -#include "compute.h" +#include "compute.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index cd64c8cb1b82d079bef98627deb65d4d243875f8..6e8aa48410e67bcad5fd19842a0f845f0bc9fc5a 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "compute_reduce_chunk.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "modify.h" @@ -25,7 +25,7 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 9074124a6111ba93893e6b3810f739382ac6d05d..8153618a88cf1c9a254cd9659270587bcc9f2fe1 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_reduce_region.h" -#include + #include "atom.h" #include "update.h" #include "modify.h" diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp index 6ff462258f631d7c7c6ac3403e377b05172acdb2..ca4b735d6e757c69284d0b230e891b54b5bdbf6a 100644 --- a/src/compute_slice.cpp +++ b/src/compute_slice.cpp @@ -12,17 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_slice.h" -#include -#include -#include -#include "update.h" -#include "modify.h" + +#include "error.h" #include "fix.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 402b84bb4b2a72124832430f35d315e7a0330a2b..6af5d2b86c79e76ba6be2599dfc7676e7d0a727a 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp index 6274ac4292d3d32aef62b0ae9146c71453b07e9b..54f052900626d8e3d2a51b93cbfbde40b8c14481 100644 --- a/src/compute_temp_chunk.cpp +++ b/src/compute_temp_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index dc12e8f6db003deb49454c3c8cb12542d02c5142..f69eaadf2bd8a916886da6d94c9a0b646b345238 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_com.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index 7d81a84bc41a9cf0079e4559937dd6796a9cf40f..b50962a2c6e3b8ab01810f3a6549032653e80967 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_deform.h" -#include + #include #include "domain.h" #include "atom.h" diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index c78e830c95668ab8530cecba96d9a50c08cd8f3b..85e51d2a5d6203ffaee67cd3d6c579d0b7dc3996 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_partial.h" -#include + #include "atom.h" #include "update.h" #include "force.h" diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp index c2ef1d5c1182bd04a23874d72f659244d743c832..eacca87e19b489f62ee649b4a87f49e7484f5aa0 100644 --- a/src/compute_temp_profile.cpp +++ b/src/compute_temp_profile.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_profile.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 187ea2454c8a2d59b1ca639572098ce5aacffedb..3874c1f286f07f4c967554ba71d97bd2fd967a0b 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_ramp.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 4c0b925eb678eb3a3fdddce8f5d97d04779fca24..74955da421eb435977d5ff4a15e046387a528491 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_region.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 786ef523ad8ebe51db6c552cccb04e34d495a5fe..6ef3038d68a3c8dadfcdd35514220d93840da7d4 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_temp_sphere.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp index 35eef8fe10a2577ceb6b15393402b7fef1b5b1f7..c0b648418b7d46af8701951edcf5ba0a44f60bd7 100644 --- a/src/compute_torque_chunk.cpp +++ b/src/compute_torque_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_torque_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp index ec19137a0e05d9740e8d9dff88d8d9772cb7037c..635c3e416108ae8559da869d1e2e73e216b52840 100644 --- a/src/compute_vacf.cpp +++ b/src/compute_vacf.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "compute_vacf.h" -#include + #include -#include + #include "atom.h" #include "update.h" #include "group.h" #include "modify.h" #include "fix_store.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp index b0a8dbeee7b5efce1b967bf8b67109fffee16222..6651110e77ee0ca1bd168d3ce639aa6d7cdd1b11 100644 --- a/src/compute_vcm_chunk.cpp +++ b/src/compute_vcm_chunk.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "compute_vcm_chunk.h" -#include + #include #include "atom.h" #include "update.h" diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index b121edb5b2868fbbf31c8532f4854897c73a64ce..7e84e9cce0d53d03c8a8caa106421ae88b3335a2 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -16,31 +16,27 @@ ------------------------------------------------------------------------- */ #include "create_atoms.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" -#include "irregular.h" -#include "modify.h" -#include "force.h" -#include "special.h" #include "domain.h" -#include "lattice.h" -#include "region.h" +#include "error.h" #include "input.h" -#include "variable.h" -#include "random_park.h" -#include "random_mars.h" -#include "math_extra.h" +#include "irregular.h" +#include "lattice.h" #include "math_const.h" -#include "error.h" +#include "math_extra.h" #include "memory.h" +#include "modify.h" +#include "molecule.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "special.h" +#include "variable.h" -#include -#include "utils.h" -#include "fmt/format.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 4261d9f7661b283adad15bbb83336597bb767a58..9e3eb65801a8ea86d3c4e99f4ed11b6a2b4e8247 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -18,21 +18,19 @@ ------------------------------------------------------------------------- */ #include "create_bonds.h" -#include -#include -#include + #include "atom.h" +#include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" -#include "comm.h" #include "group.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "special.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 7dcc4748e91e26c94b6551b950e3fe185debca57..8baee645cf1e3293ec9b39b0b1486875cfd60a4b 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -12,33 +12,30 @@ ------------------------------------------------------------------------- */ #include "delete_atoms.h" -#include -#include -#include + #include "atom.h" #include "atom_vec.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" -#include "molecule.h" #include "comm.h" #include "domain.h" +#include "error.h" #include "force.h" #include "group.h" -#include "region.h" +#include "memory.h" #include "modify.h" -#include "neighbor.h" +#include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" +#include "neighbor.h" #include "random_mars.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "region.h" +#include #include -#include +#include using namespace LAMMPS_NS; diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index f08c94a2734ef4625a9b5d14e312bd91eadbae99..b8ec5f78835860ab76da1bc77a18a1878882a5f2 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -12,20 +12,17 @@ ------------------------------------------------------------------------- */ #include "delete_bonds.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "group.h" #include "special.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/deprecated.cpp b/src/deprecated.cpp index dc0ab400d4f3374676b5fe8dcaf4a395a666f50d..ab9cc8cf4432b138bc5ceff9eb78c6a82acbc116 100644 --- a/src/deprecated.cpp +++ b/src/deprecated.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "deprecated.h" -#include + #include "comm.h" #include "error.h" #include "input.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 1709f7d3d743c3afebc7efbc280cbebfafd5474a..91ef3e8e9ef05fcb17219c8f983987cf782b74cc 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_deprecated.h" -#include -#include "dihedral_hybrid.h" + #include "comm.h" -#include "force.h" +#include "dihedral_hybrid.h" #include "error.h" -#include "utils.h" +#include "force.h" + using namespace LAMMPS_NS; diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index 8f41b30d56e60620f637e7c568a99411aaafdd29..61e0fdc72af23931dd14dd01b4b18193e808a885 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "dihedral_hybrid.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 59167ca30e8a7db35f06e23b348d8cc488843145..9570590c098bb70beba142382645cb08a4a2cc77 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "dihedral_zero.h" -#include + #include "atom.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index a30ac2c2b2d75d7b0c8ebbb9f0fa465bfb5f6131..018288d470ad1b59bba622599e0073a5ca68ccde 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -12,30 +12,28 @@ ------------------------------------------------------------------------- */ #include "displace_atoms.h" -#include -#include -#include + #include "atom.h" -#include "modify.h" -#include "domain.h" -#include "lattice.h" -#include "comm.h" -#include "irregular.h" -#include "group.h" -#include "math_const.h" -#include "random_park.h" -#include "force.h" -#include "input.h" -#include "variable.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "input.h" +#include "irregular.h" +#include "lattice.h" +#include "math_const.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "random_park.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/domain.cpp b/src/domain.cpp index 81de88d1eed83bea807bf42355fe49e44caf6697..984c735a2007a3ceb4d67871893981c7dd4d0007 100644 --- a/src/domain.cpp +++ b/src/domain.cpp @@ -16,30 +16,28 @@ ------------------------------------------------------------------------- */ #include "domain.h" -#include -#include -#include -#include -#include "style_region.h" +#include "style_region.h" // IWYU pragma: keep + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "kspace.h" -#include "update.h" -#include "modify.h" +#include "comm.h" +#include "error.h" #include "fix.h" #include "fix_deform.h" -#include "region.h" +#include "force.h" +#include "kspace.h" #include "lattice.h" -#include "comm.h" +#include "memory.h" +#include "modify.h" +#include "molecule.h" #include "output.h" +#include "region.h" #include "thermo.h" #include "universe.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -108,7 +106,8 @@ Domain::Domain(LAMMPS *lmp) : Pointers(lmp) #define REGION_CLASS #define RegionStyle(key,Class) \ (*region_map)[#key] = ®ion_creator; -#include "style_region.h" +#include "style_region.h" // IWYU pragma: keep + #undef RegionStyle #undef REGION_CLASS } diff --git a/src/domain.h b/src/domain.h index 58b935ce01f1502cd235797d44f7ac04085af508..d807463bf3b44f0e91024b66431adc4a4661f7bc 100644 --- a/src/domain.h +++ b/src/domain.h @@ -14,12 +14,13 @@ #ifndef LMP_DOMAIN_H #define LMP_DOMAIN_H +#include "pointers.h" + #include #include -#include -#include "pointers.h" namespace LAMMPS_NS { + class Region; class Domain : protected Pointers { public: @@ -90,7 +91,7 @@ class Domain : protected Pointers { int nregion; // # of defined Regions int maxregion; // max # list can hold - class Region **regions; // list of defined Regions + Region **regions; // list of defined Regions int copymode; enum{NO_REMAP,X_REMAP,V_REMAP}; diff --git a/src/dump.cpp b/src/dump.cpp index 0698a84e81baf35f68595ca4757312ece2479170..ecb87b79fd5753e94aa33ef58929cee681506078 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -12,21 +12,21 @@ ------------------------------------------------------------------------- */ #include "dump.h" -#include -#include + #include "atom.h" #include "irregular.h" #include "update.h" #include "domain.h" #include "group.h" #include "output.h" -#include "force.h" #include "modify.h" #include "fix.h" #include "compute.h" #include "memory.h" #include "error.h" +#include + using namespace LAMMPS_NS; #if defined(LMP_QSORT) diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 3b0594a2cb0f4202c2b5f948c66c43e2b9a8a2f6..167d88789c0a515f04c0fbda6bf19a2e5a203986 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -12,25 +12,22 @@ ------------------------------------------------------------------------- */ #include "dump_custom.h" -#include -#include -#include + #include "atom.h" -#include "force.h" -#include "domain.h" -#include "region.h" -#include "group.h" -#include "input.h" -#include "modify.h" #include "compute.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_store.h" +#include "group.h" +#include "input.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "region.h" #include "update.h" #include "variable.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/dump_deprecated.cpp b/src/dump_deprecated.cpp index 822bed78328ad350a924a1177a5e6734bc4f33b0..ed8336eebcef4cc2344fe497e3663ffabbe353d0 100644 --- a/src/dump_deprecated.cpp +++ b/src/dump_deprecated.cpp @@ -12,10 +12,9 @@ ------------------------------------------------------------------------- */ #include "dump_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/dump_image.cpp b/src/dump_image.cpp index ea9fb612cb3f2bdd34e1ba606efcfb33e47ff029..96a338950b232b54e8bf248210530ee2f9634bed 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "dump_image.h" -#include + #include #include #include @@ -35,7 +35,7 @@ #include "math_extra.h" #include "error.h" #include "memory.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 666a7773bda350ad5b92297add4c7e425f950478..a71166ec574924f39d033a1b4d1cf721e231e375 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -12,19 +12,16 @@ ------------------------------------------------------------------------- */ #include "dump_local.h" -#include -#include -#include -#include "modify.h" -#include "fix.h" + #include "compute.h" #include "domain.h" -#include "update.h" -#include "input.h" -#include "memory.h" #include "error.h" -#include "force.h" -#include "utils.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp index 4966310470aae54bac541b12a2ff3649a7b76493..5f6d0b80d7c026eb2e2a741d9d2affc53d2f33ba 100644 --- a/src/dump_movie.cpp +++ b/src/dump_movie.cpp @@ -16,11 +16,11 @@ ------------------------------------------------------------------------- */ #include "dump_movie.h" -#include + #include "comm.h" -#include "force.h" #include "error.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/error.cpp b/src/error.cpp index 7458f816c091861f837db53147f127ee9113f943..0ea218887f66e70a35741088c50e1bb294fb15e9 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -12,16 +12,11 @@ ------------------------------------------------------------------------- */ #include "error.h" -#include -#include -#include -#include -#include "universe.h" -#include "output.h" -#include "input.h" + #include "accelerator_kokkos.h" -#include "utils.h" -#include "fmt/format.h" +#include "input.h" +#include "output.h" +#include "universe.h" #if defined(LAMMPS_EXCEPTIONS) #include "update.h" diff --git a/src/error.h b/src/error.h index 40c1559464a89ad6b4d7a692255c6f497e41c7d6..dedebc414822eb253b7a36adb92ae81c15b59e43 100644 --- a/src/error.h +++ b/src/error.h @@ -15,7 +15,6 @@ #define LMP_ERROR_H #include "pointers.h" -#include #ifdef LAMMPS_EXCEPTIONS #include "exceptions.h" diff --git a/src/finish.cpp b/src/finish.cpp index 51f886b5dbb1b790b92c6c1183aa7050144069b1..3bfe3a7bbfde666cdf79c6fe2b1bfd67cfcd462b 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -12,28 +12,26 @@ ------------------------------------------------------------------------- */ #include "finish.h" -#include -#include -#include -#include + #include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" +#include "memory.h" // IWYU pragma: keep #include "min.h" -#include "neighbor.h" +#include "molecule.h" #include "neigh_list.h" #include "neigh_request.h" -#include "memory.h" -#include "error.h" -#include "timer.h" +#include "neighbor.h" // IWYU pragma: keep +#include "timer.h" // IWYU pragma: keep #include "universe.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include #ifdef LMP_USER_OMP #include "modify.h" diff --git a/src/fix.cpp b/src/fix.cpp index 549208a0ce9fd5232dfc5e2ffd743a194319b1bc..03313739a11e0a2e496bab771f551197f36678aa 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix.h" -#include -#include + #include "atom.h" -#include "group.h" -#include "force.h" #include "atom_masks.h" -#include "memory.h" #include "error.h" +#include "group.h" +#include "memory.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index c07b225f9ddaaf01d170464037401f0e227e747c..dba4fde07759d885dde5e68e0d0678a5c20ad491 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -30,8 +30,8 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp index d5c1bbef2914064eeac5ba69bd15fbb3e5b65455..0983728ea91e757f3c6b2760fc8a92a6159f11f9 100644 --- a/src/fix_addforce.cpp +++ b/src/fix_addforce.cpp @@ -12,21 +12,20 @@ ------------------------------------------------------------------------- */ #include "fix_addforce.h" -#include -#include -#include + #include "atom.h" #include "atom_masks.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp index a8d78f14e7714897b42fef9a6cd8c284e50db435..da009c55d5982e48db410c92369ffe8fb6bd6db2 100644 --- a/src/fix_ave_atom.cpp +++ b/src/fix_ave_atom.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "fix_ave_atom.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" -#include "utils.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp index dd753ddc2dcd7eb3e098010d8d051ed2675f9825..18fb33527938cbea7680da75d936d60edc823b90 100644 --- a/src/fix_ave_chunk.cpp +++ b/src/fix_ave_chunk.cpp @@ -12,8 +12,8 @@ ------------------------------------------------------------------------- */ #include "fix_ave_chunk.h" -#include -#include + + #include #include #include "atom.h" @@ -27,8 +27,8 @@ #include "variable.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp index 293b7fc2968394d9f1e07864b71c561c118f2f06..031dfc26bff713ef5171b5e2c55a737aaf94b953 100644 --- a/src/fix_ave_correlate.cpp +++ b/src/fix_ave_correlate.cpp @@ -18,20 +18,17 @@ ------------------------------------------------------------------------- */ #include "fix_ave_correlate.h" -#include -#include -#include -#include -#include "update.h" -#include "modify.h" + #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 091ec19fffa454083c98744f09fadb25096bfbf9..3a9346498fb4c7228ed1ffb309c1694d539ee551 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -12,21 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_ave_histo.h" -#include -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 4b86681153d0175d5d60184bc60a79d86acce661..5e93df0313732c88653eb766e1b84f53aa805064 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -15,7 +15,7 @@ Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ #include "fix_ave_histo_weight.h" -#include + #include #include "fix.h" #include "atom.h" diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp index 4cc8cc3d3d7a9f12cccfa386f08c3c8bfff17f21..9c493b98462e7b40dd992d6c6836afaea7212d33 100644 --- a/src/fix_ave_time.cpp +++ b/src/fix_ave_time.cpp @@ -16,20 +16,17 @@ ------------------------------------------------------------------------- */ #include "fix_ave_time.h" -#include -#include -#include -#include -#include "update.h" -#include "force.h" -#include "modify.h" + #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp index b5b2527e2599108ec419d7c1b93e22adba444d17..00ec0d67ba967f9fd0da0cffbe871ffdf1e0aff6 100644 --- a/src/fix_aveforce.cpp +++ b/src/fix_aveforce.cpp @@ -12,18 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_aveforce.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp index 39760e947924725dd2639e7bf3a5963bbdf7dc0a..5fd9ef190e8638da8809e3921fd2ef60f1bbd229 100644 --- a/src/fix_box_relax.cpp +++ b/src/fix_box_relax.cpp @@ -18,7 +18,7 @@ #include "fix_box_relax.h" #include #include -#include + #include "atom.h" #include "domain.h" #include "update.h" @@ -29,7 +29,7 @@ #include "compute.h" #include "error.h" #include "math_extra.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 4b12c393cb2653b5b052bc40cdbd6866b760aaf2..92fd42f3dbaa1fb4feabae68e2909d2777260ae9 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_controller.h" -#include -#include -#include "force.h" -#include "update.h" -#include "modify.h" + #include "compute.h" +#include "error.h" #include "input.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp index d3ceb69ea07fde43d68affd2abc63721d1721a84..877eac0524f1692991937e0f695a9aca2205dccc 100644 --- a/src/fix_deprecated.cpp +++ b/src/fix_deprecated.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "fix_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp index 5b74b75fcd5781ec05302de3fdc4188ea4f9bc15..240001456948434467e057b0c3191e8e2229882a 100644 --- a/src/fix_drag.cpp +++ b/src/fix_drag.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_drag.h" -#include -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 8fb4f0cdfc25a50d703f47338e07fc9bee6c4ac5..360f0d29982e876d5e35b69c1771ebdfc3af1fde 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_dt_reset.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 7dd8c082047c6dd7db4271e931e44dbbc50e6812..be2a74d81b2af00f87200b2bb39f513c082185e1 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -19,7 +19,7 @@ #include "modify.h" #include "respa.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 5d810ff38be356a0ffffa63605597c74dc962fd6..1db7e15295ca0347c3c40fe2fe1b66da93afb9f3 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_external.h" -#include + #include "atom.h" -#include "update.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "memory.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp index 82b831196819a56ee15837c3b7d0e9f1c17b0946..6dff9373850a3ff957229b00c14530fe37bd6ab6 100644 --- a/src/fix_gravity.cpp +++ b/src/fix_gravity.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ #include "fix_gravity.h" -#include -#include -#include + #include "atom.h" -#include "update.h" #include "domain.h" -#include "respa.h" -#include "modify.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "math_const.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 5e2a12c988fcd6c0d5abce875a8521e54af0cedf..bb51fafa12618d84e7b63b7fcc2aca77b726e581 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -12,20 +12,21 @@ ------------------------------------------------------------------------- */ #include "fix_group.h" -#include -#include "group.h" -#include "update.h" + #include "atom.h" -#include "force.h" #include "comm.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "group.h" +#include "input.h" +#include "memory.h" #include "modify.h" +#include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp index cf39ba61e205c0c6275af7361c76cb546d624e80..f8222e3ece3c3bd7995dbe5d898ffd90d776ba41 100644 --- a/src/fix_halt.cpp +++ b/src/fix_halt.cpp @@ -12,21 +12,19 @@ ------------------------------------------------------------------------- */ #include "fix_halt.h" -#include -#include -#include -#include -#include "update.h" -#include "force.h" -#include "input.h" -#include "variable.h" + #include "atom.h" -#include "neighbor.h" -#include "modify.h" #include "comm.h" -#include "timer.h" #include "error.h" -#include "fmt/format.h" +#include "input.h" +#include "modify.h" +#include "neighbor.h" +#include "timer.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 7fbdd24b4c94c2c4da6b34def78ae8cfb13f5a44..e2eb3993227d21daa978f6359d19461261de791d 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_heat.h" -#include + #include #include #include "atom.h" diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp index dcddad95b21ae6aab84ec3aeb199ee7691ac8e73..ae58f27913ad833f8fb5495ca9e622b621ff7624 100644 --- a/src/fix_indent.cpp +++ b/src/fix_indent.cpp @@ -16,19 +16,19 @@ ------------------------------------------------------------------------- */ #include "fix_indent.h" -#include -#include -#include + #include "atom.h" -#include "input.h" -#include "variable.h" #include "domain.h" +#include "error.h" +#include "input.h" #include "lattice.h" -#include "update.h" #include "modify.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index 81c186c703a6bbaea5784944fb9cd49de9ad3dd2..9d0b5f28f1aee47be32a59cf26a958d7c268ccff 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -20,7 +20,7 @@ ------------------------------------------------------------------------- */ #include "fix_langevin.h" -#include + #include #include #include "math_extra.h" @@ -38,7 +38,7 @@ #include "memory.h" #include "error.h" #include "group.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 0287c8c0dbc06412ca8e13bc9c8e216899533545..cacec13302de9fcd20adbef75d5f348f610f37a4 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_lineforce.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp index c1056d2b1660a4fce56485141d489b726c2e9673..259099e07c731cda812ef7dc87fc253b849c46ae 100644 --- a/src/fix_momentum.cpp +++ b/src/fix_momentum.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_momentum.h" -#include -#include -#include + #include "atom.h" #include "domain.h" -#include "group.h" #include "error.h" -#include "force.h" +#include "group.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp index d951a924fe6764dbb5a255bce5e544f5b883c93c..43415a6ef5bd53858d942c94329b6a5f73ba3b59 100644 --- a/src/fix_neigh_history.cpp +++ b/src/fix_neigh_history.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_neigh_history.h" -#include + #include #include "my_page.h" #include "atom.h" diff --git a/src/fix_nh.h b/src/fix_nh.h index 624b0c8bb469166744fa81254c96afc32d311e6b..f137ecbe558ae83240132291fb351856d85aeeea 100644 --- a/src/fix_nh.h +++ b/src/fix_nh.h @@ -14,7 +14,7 @@ #ifndef LMP_FIX_NH_H #define LMP_FIX_NH_H -#include "fix.h" +#include "fix.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp index 1ff3fc2d4d90824fb78aa4e710d0c73f43b6bf36..d60798e007e276f2b0ddb3d15416f60ad230d36b 100644 --- a/src/fix_nh_sphere.cpp +++ b/src/fix_nh_sphere.cpp @@ -16,15 +16,16 @@ ------------------------------------------------------------------------- */ #include "fix_nh_sphere.h" -#include -#include + #include "atom.h" -#include "atom_vec.h" +#include "domain.h" #include "error.h" #include "force.h" -#include "domain.h" -#include "math_vector.h" #include "math_extra.h" +#include "math_vector.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp index 9251ce384e5e13f18481e2303919a72400109919..f4ff71d3a3d1c76522d5954be4ff09ccaaad911d 100644 --- a/src/fix_nph.cpp +++ b/src/fix_nph.cpp @@ -13,7 +13,7 @@ #include "fix_nph.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index cf2298f5f89db845a63970ca02106383600ad044..b49eb0c5c5977b7068aeb4fa41c105edce889d3a 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -13,7 +13,7 @@ #include "fix_nph_sphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp index 6949ead1d6b0480d1cb654d613d794dd2d3671a1..f6ec24991b1a99c603eb852dfac02a37a893531f 100644 --- a/src/fix_npt.cpp +++ b/src/fix_npt.cpp @@ -13,7 +13,7 @@ #include "fix_npt.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index e38d88fadd0f8456225c6bd22dac4ade8e55ea89..1bd879c786413d44d0f0cba65bcbcc4d4ecc6f8e 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -13,7 +13,7 @@ #include "fix_npt_sphere.h" #include -#include + #include "modify.h" #include "error.h" diff --git a/src/fix_numdiff.cpp b/src/fix_numdiff.cpp index f6d064b794c168e8e26374502fa88a5caf02e693..145d60e8df57fbd6ca48cb8af9ada9e2a0ae0702 100644 --- a/src/fix_numdiff.cpp +++ b/src/fix_numdiff.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "fix_numdiff.h" -#include + #include #include "atom.h" #include "domain.h" diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 83a6af5d0cbb3ea1c3ff5a890c0e2bd08aa6a32c..ed79c6b21b0cd46548d693c02f9f27368380e3a6 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "fix_nve_limit.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "modify.h" #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp index c0fea17c2bb7f41e41d9da44dff0addca7875918..87fba3eca3de05c4a8f11c557168aeaf3340b208 100644 --- a/src/fix_nve_sphere.cpp +++ b/src/fix_nve_sphere.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "fix_nve_sphere.h" -#include -#include + #include "atom.h" #include "domain.h" -#include "atom_vec.h" -#include "force.h" #include "error.h" -#include "math_vector.h" +#include "force.h" #include "math_extra.h" +#include "math_vector.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp index 7868693b697dbd62df3934ebe3d2097dd8f218aa..f7a53cf382a0f72a6907754bd1504a77daf17709 100644 --- a/src/fix_nvt.cpp +++ b/src/fix_nvt.cpp @@ -13,11 +13,11 @@ #include "fix_nvt.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index ccf7aaecaffee1aac0eb02295878bbe35af47d29..3cc88772d74017f6f3f434756f0400765a167178 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -26,7 +26,7 @@ #include "fix_deform.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp index 40c3ba19e3acc8afbeeb12a6bf48afd725cad61b..7c4159455f7f3095144f69ceb1ce8200448e534e 100644 --- a/src/fix_nvt_sphere.cpp +++ b/src/fix_nvt_sphere.cpp @@ -13,11 +13,11 @@ #include "fix_nvt_sphere.h" #include -#include + #include "group.h" #include "modify.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 9434a4b348a7f62ff2ff986de1fdd8a9603c6806..2e3bcadd69b39146314c307d72d9960b1ce03d5c 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_planeforce.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp index a430130fe47ce2a5004b0d390beba0a92497af14..a90bf86c56a3ea0898f8c5aebcede87a030d5918 100644 --- a/src/fix_press_berendsen.cpp +++ b/src/fix_press_berendsen.cpp @@ -14,7 +14,7 @@ #include "fix_press_berendsen.h" #include #include -#include + #include "atom.h" #include "force.h" #include "comm.h" diff --git a/src/fix_print.cpp b/src/fix_print.cpp index 8964a9ba8256a4218878661a49e8e6b7ca25f306..78fceea1841dbeb4d0063cefb88ae4ae6398e071 100644 --- a/src/fix_print.cpp +++ b/src/fix_print.cpp @@ -12,17 +12,15 @@ ------------------------------------------------------------------------- */ #include "fix_print.h" -#include -#include -#include "update.h" + +#include "error.h" #include "input.h" +#include "memory.h" #include "modify.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp index 374d0069fd50c7a9e8bfc393c190a652683ccdb7..07108721c48ef684f7c5a4ce75d07e5427fb2385 100644 --- a/src/fix_property_atom.cpp +++ b/src/fix_property_atom.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "fix_property_atom.h" -#include + #include #include "atom.h" #include "comm.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp index c1c01501773a3d4335edb1dd0e5f88de96b29e87..2e10b15ffa75b6ade309a0d976baab9accc3d4c4 100644 --- a/src/fix_read_restart.cpp +++ b/src/fix_read_restart.cpp @@ -12,9 +12,9 @@ ------------------------------------------------------------------------- */ #include "fix_read_restart.h" + #include "atom.h" #include "memory.h" -#include "force.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp index 8997e4b8056c7658a171a9971aca7f20180b071f..3f9eec9ee47eb45f5b702b0130adac178ca30a5d 100644 --- a/src/fix_recenter.cpp +++ b/src/fix_recenter.cpp @@ -16,18 +16,19 @@ ------------------------------------------------------------------------- */ #include "fix_recenter.h" -#include -#include + #include "atom.h" -#include "group.h" -#include "update.h" +#include "comm.h" #include "domain.h" +#include "error.h" +#include "group.h" #include "lattice.h" #include "modify.h" -#include "comm.h" #include "respa.h" -#include "error.h" -#include "force.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp index 459b30c1b218de733cbde8a66ffb54bdce3c2309..b116f8ccac71d3bbd51225aed3cb46cea572e229 100644 --- a/src/fix_respa.cpp +++ b/src/fix_respa.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_respa.h" -#include + #include "atom.h" -#include "force.h" #include "memory.h" +#include + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index 305ee0ea26eabb5afc162a52f4cd815987332804..4f675bf7bf20e3d56a979c37d9f5e838bf65cec7 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_restrain.h" -#include + #include #include #include "atom.h" @@ -29,7 +29,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp index 1a3158ed4cfde5fc5ebbf1c4eb1c97ef32672dbb..229890c5df7eb6cc1b5a5f9e67207844d7d88b74 100644 --- a/src/fix_setforce.cpp +++ b/src/fix_setforce.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ #include "fix_setforce.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "modify.h" #include "domain.h" +#include "error.h" +#include "input.h" +#include "memory.h" +#include "modify.h" #include "region.h" #include "respa.h" -#include "input.h" +#include "update.h" #include "variable.h" -#include "memory.h" -#include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp index 1bd76f5c55ceb42cd366866d575488aea1c6da15..2d695add269c413160ea823606a789aafc6025e1 100644 --- a/src/fix_spring.cpp +++ b/src/fix_spring.cpp @@ -16,14 +16,15 @@ ------------------------------------------------------------------------- */ #include "fix_spring.h" -#include -#include + #include "atom.h" -#include "update.h" -#include "respa.h" -#include "force.h" -#include "group.h" #include "error.h" +#include "group.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp index 778a6f0c435345e6338ef114c11ad40246ac41a2..d8de88bd637b8b47c85cc6bcaa6ecb16b379fb14 100644 --- a/src/fix_spring_chunk.cpp +++ b/src/fix_spring_chunk.cpp @@ -12,18 +12,19 @@ ------------------------------------------------------------------------- */ #include "fix_spring_chunk.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "force.h" -#include "respa.h" -#include "modify.h" #include "compute_chunk_atom.h" #include "compute_com_chunk.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp index e3ba935340afc7694a2f5dd0ad585e57ffa8ce56..5715e7eb887035e146a1fb61d886f7d374de5224 100644 --- a/src/fix_spring_rg.cpp +++ b/src/fix_spring_rg.cpp @@ -17,15 +17,16 @@ ------------------------------------------------------------------------- */ #include "fix_spring_rg.h" -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "group.h" -#include "respa.h" #include "domain.h" #include "error.h" -#include "force.h" +#include "group.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp index fef7e2086cb5992867642b135fc48f11556c2624..8e7b3eb925492f8fd1c912466cb66eaabce28f05 100644 --- a/src/fix_spring_self.cpp +++ b/src/fix_spring_self.cpp @@ -16,15 +16,15 @@ ------------------------------------------------------------------------- */ #include "fix_spring_self.h" -#include -#include + #include "atom.h" -#include "update.h" #include "domain.h" -#include "respa.h" -#include "memory.h" #include "error.h" -#include "force.h" +#include "memory.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 8ce94fb54aa185af6ac8cd03f8d89eac8141dd4a..3eb20752504dac4026d21f22db6f0594fe44edc0 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_store.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "memory.h" #include "error.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp index 60a1a70037f0d83efca246dfab3b9b21ad684d56..fd4563b7ada48a2d311cc0e171458cc991509c56 100644 --- a/src/fix_store_state.cpp +++ b/src/fix_store_state.cpp @@ -12,20 +12,20 @@ ------------------------------------------------------------------------- */ #include "fix_store_state.h" -#include -#include + #include "atom.h" -#include "domain.h" -#include "update.h" -#include "group.h" -#include "modify.h" #include "compute.h" +#include "domain.h" +#include "error.h" #include "fix.h" +#include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "force.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp index 5016b8c3437c9ac8159571feb43a8e5f46519912..ec2965d072f668dd7cae71f52deb541307e92e5c 100644 --- a/src/fix_temp_berendsen.cpp +++ b/src/fix_temp_berendsen.cpp @@ -13,7 +13,7 @@ #include "fix_temp_berendsen.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "modify.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp index 5a7b9a04dbb76d0fbe2513e79be4794b53bcd4bc..cf7e9e9fe289b49d3cfcd4011e715783ee41833d 100644 --- a/src/fix_temp_csld.cpp +++ b/src/fix_temp_csld.cpp @@ -17,7 +17,7 @@ #include "fix_temp_csld.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -31,7 +31,7 @@ #include "compute.h" #include "random_mars.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 72e4dd635d77ce26d89e648eb81b3aa5a9edf655..c6209051028df466b4a0bf26a78f55c3904e7612 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -17,10 +17,10 @@ ------------------------------------------------------------------------- */ #include "fix_temp_csvr.h" -#include + #include #include -#include + #include "atom.h" #include "force.h" #include "comm.h" @@ -32,7 +32,7 @@ #include "compute.h" #include "random_mars.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp index e575d72f7faf2b3a441a5edf241ea92ebac46e3d..b5cb9c9a1b54e3f8350401c8c669e248949d1862 100644 --- a/src/fix_temp_rescale.cpp +++ b/src/fix_temp_rescale.cpp @@ -13,7 +13,7 @@ #include "fix_temp_rescale.h" #include -#include + #include #include "atom.h" #include "force.h" @@ -25,7 +25,7 @@ #include "modify.h" #include "compute.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp index 98fb373075d08a0f782c690efd08ddb73bcd6ed4..12e36d890e95e6a992f7ca1946fbc9d02e4ced3b 100644 --- a/src/fix_tmd.cpp +++ b/src/fix_tmd.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "fix_tmd.h" -#include + #include #include #include "atom.h" @@ -29,8 +29,8 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + + using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index 48f14f5e2f2567bf8633d12988a5ac330b094e9d..6bcdfe948e7af095fbee19fc12159c7d5708fbf4 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -12,16 +12,16 @@ ------------------------------------------------------------------------- */ #include "fix_vector.h" -#include -#include -#include "update.h" -#include "force.h" -#include "modify.h" + #include "compute.h" +#include "error.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp index 7d532d832d8c768b933bcda846302c29ca0f19f2..08649280d87c30a23a475cc33941f8d4893ba58b 100644 --- a/src/fix_viscous.cpp +++ b/src/fix_viscous.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_viscous.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" -#include "force.h" +#include "respa.h" +#include "update.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp index 0c343938abdca9dd8eccbeb98805ff7863a9b4b2..cb822f10909cc2eec8d2dd968d30353f11724490 100644 --- a/src/fix_wall.cpp +++ b/src/fix_wall.cpp @@ -12,18 +12,17 @@ ------------------------------------------------------------------------- */ #include "fix_wall.h" -#include -#include -#include "input.h" -#include "variable.h" + #include "domain.h" +#include "error.h" +#include "input.h" #include "lattice.h" -#include "update.h" #include "modify.h" #include "respa.h" -#include "error.h" -#include "force.h" -#include "utils.h" +#include "update.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp index 061083e55c5ebd0d63614b04b41bf6c4ffc0c4ce..227ef66564b227cfa15bbde22b513634da6b84d3 100644 --- a/src/fix_wall_reflect.cpp +++ b/src/fix_wall_reflect.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "fix_wall_reflect.h" -#include + #include "atom.h" #include "comm.h" -#include "update.h" -#include "modify.h" #include "domain.h" -#include "force.h" -#include "lattice.h" +#include "error.h" #include "input.h" +#include "lattice.h" +#include "modify.h" +#include "update.h" #include "variable.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp index e60b3b4aada60055d67202144fc99347e59ae477..fc3735cfbfb6f49082644753346f88f80fa09e1a 100644 --- a/src/fix_wall_region.cpp +++ b/src/fix_wall_region.cpp @@ -12,17 +12,17 @@ ------------------------------------------------------------------------- */ #include "fix_wall_region.h" -#include -#include -#include + #include "atom.h" #include "domain.h" -#include "region.h" -#include "force.h" -#include "update.h" -#include "respa.h" #include "error.h" #include "math_const.h" +#include "region.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/force.cpp b/src/force.cpp index 10b82afabe9926586657a02d74e2133ac9f42b5d..701113d7eff4101adb57d865fd83ee1a4aeb8303 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -12,31 +12,27 @@ ------------------------------------------------------------------------- */ #include "force.h" -#include -#include -#include -#include -#include "style_bond.h" -#include "style_angle.h" -#include "style_dihedral.h" -#include "style_improper.h" -#include "style_pair.h" -#include "style_kspace.h" +#include "style_angle.h" // IWYU pragma: keep +#include "style_bond.h" // IWYU pragma: keep +#include "style_dihedral.h" // IWYU pragma: keep +#include "style_improper.h" // IWYU pragma: keep +#include "style_kspace.h" // IWYU pragma: keep +#include "style_pair.h" // IWYU pragma: keep + +#include "angle.h" #include "atom.h" -#include "comm.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "pair_hybrid_overlay.h" #include "bond.h" #include "bond_hybrid.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "error.h" #include "improper.h" #include "kspace.h" -#include "error.h" -#include "update.h" -#include "utils.h" -#include "fmt/format.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "pair_hybrid_overlay.h" + +#include using namespace LAMMPS_NS; diff --git a/src/force.h b/src/force.h index d7824ea90eced834ac701749113a252100e1612a..1302e20f124f3fd8267cfa2f01cb3f8f75aa423b 100644 --- a/src/force.h +++ b/src/force.h @@ -15,10 +15,16 @@ #define LMP_FORCE_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { + class Angle; + class Bond; + class Dihedral; + class Improper; + class KSpace; + class Pair; class Force : protected Pointers { public: @@ -47,23 +53,23 @@ class Force : protected Pointers { int newton,newton_pair,newton_bond; // Newton's 3rd law settings - class Pair *pair; + Pair *pair; char *pair_style; char *pair_restart; - class Bond *bond; + Bond *bond; char *bond_style; - class Angle *angle; + Angle *angle; char *angle_style; - class Dihedral *dihedral; + Dihedral *dihedral; char *dihedral_style; - class Improper *improper; + Improper *improper; char *improper_style; - class KSpace *kspace; + KSpace *kspace; char *kspace_style; typedef Pair *(*PairCreator)(LAMMPS *); @@ -102,29 +108,29 @@ class Force : protected Pointers { void setup(); void create_pair(const std::string &, int); - class Pair *new_pair(const std::string &, int, int &); - class Pair *pair_match(const std::string &, int, int nsub=0); + Pair *new_pair(const std::string &, int, int &); + Pair *pair_match(const std::string &, int, int nsub=0); char *pair_match_ptr(Pair *); void create_bond(const std::string &, int); - class Bond *new_bond(const std::string &, int, int &); - class Bond *bond_match(const std::string &); + Bond *new_bond(const std::string &, int, int &); + Bond *bond_match(const std::string &); void create_angle(const std::string &, int); - class Angle *new_angle(const std::string &, int, int &); - class Angle *angle_match(const std::string &); + Angle *new_angle(const std::string &, int, int &); + Angle *angle_match(const std::string &); void create_dihedral(const std::string &, int); - class Dihedral *new_dihedral(const std::string &, int, int &); - class Dihedral *dihedral_match(const std::string &); + Dihedral *new_dihedral(const std::string &, int, int &); + Dihedral *dihedral_match(const std::string &); void create_improper(const std::string &, int); - class Improper *new_improper(const std::string &, int, int &); - class Improper *improper_match(const std::string &); + Improper *new_improper(const std::string &, int, int &); + Improper *improper_match(const std::string &); void create_kspace(const std::string &, int); - class KSpace *new_kspace(const std::string &, int, int &); - class KSpace *kspace_match(const std::string &, int); + KSpace *new_kspace(const std::string &, int, int &); + KSpace *kspace_match(const std::string &, int); void store_style(char *&, const std::string &, int); void set_special(int, char **); diff --git a/src/group.cpp b/src/group.cpp index 2377f028bdba360c0045e536c18c9ad7bed78a21..a2e20a6ab173ba2a07dcbf22e053c61dddd1d226 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -12,30 +12,28 @@ ------------------------------------------------------------------------- */ #include "group.h" -#include -#include -#include -#include -#include -#include "domain.h" + #include "atom.h" -#include "force.h" #include "comm.h" -#include "region.h" -#include "modify.h" -#include "fix.h" #include "compute.h" -#include "output.h" -#include "input.h" -#include "variable.h" +#include "domain.h" #include "dump.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "input.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "output.h" +#include "region.h" +#include "variable.h" +#include +#include #include +#include +#include using namespace LAMMPS_NS; @@ -538,7 +536,7 @@ void Group::assign(int narg, char **arg) void Group::assign(const std::string &groupcmd) { - std::vector args = utils::split_words(groupcmd); + auto args = utils::split_words(groupcmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { diff --git a/src/group.h b/src/group.h index b9a5c27140846a87bc95b9d22a6548afb1ab9bfe..39c446d119e8831345c2824f362927b0fccfc7d2 100644 --- a/src/group.h +++ b/src/group.h @@ -15,8 +15,8 @@ #define LMP_GROUP_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/image.cpp b/src/image.cpp index 56d9bc301a9077f55f3f82fb66093ff4d407f845..755be587d887e3de11b7d3c101232e4c781f85e1 100644 --- a/src/image.cpp +++ b/src/image.cpp @@ -16,16 +16,16 @@ ------------------------------------------------------------------------- */ #include "image.h" -#include -#include -#include -#include -#include "math_extra.h" -#include "random_mars.h" -#include "math_const.h" + #include "error.h" -#include "force.h" +#include "math_const.h" +#include "math_extra.h" #include "memory.h" +#include "random_mars.h" + +#include +#include +#include #ifdef LAMMPS_JPEG #include diff --git a/src/imbalance_group.cpp b/src/imbalance_group.cpp index 72b102879152941f3233b13cc68bab639fc8c59f..f604f150b52bef92d18746378bacb75fca8c6de8 100644 --- a/src/imbalance_group.cpp +++ b/src/imbalance_group.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "imbalance_group.h" + #include "atom.h" -#include "force.h" -#include "group.h" #include "error.h" -#include -#include "fmt/format.h" +#include "group.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_neigh.cpp b/src/imbalance_neigh.cpp index 0beb62bdb41941bdff00033c2dfc71602ce74dc5..70d5580b9c58ea7e588da14f7e10c9d793798c8a 100644 --- a/src/imbalance_neigh.cpp +++ b/src/imbalance_neigh.cpp @@ -12,15 +12,13 @@ ------------------------------------------------------------------------- */ #include "imbalance_neigh.h" -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "error.h" -#include "fmt/format.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 919d1f3f6150a85c26e74922fe30e234c0910ea6..2661b57b25f0663327536a075d3d25e975afae56 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "imbalance_store.h" -#include + #include "atom.h" #include "error.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/imbalance_time.cpp b/src/imbalance_time.cpp index 99e549e90ec0cec2aabd381c521c99dc67255caf..438728ef3ef751cde05e5e0d0296ad7646877a6b 100644 --- a/src/imbalance_time.cpp +++ b/src/imbalance_time.cpp @@ -12,12 +12,10 @@ ------------------------------------------------------------------------- */ #include "imbalance_time.h" -#include + #include "atom.h" -#include "force.h" -#include "timer.h" #include "error.h" -#include "fmt/format.h" +#include "timer.h" using namespace LAMMPS_NS; diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index d1a76ed9f7c122d7b35faef2b305c5b08df93718..a2c940789e43379fe30de3abab21c6f11ea09fbc 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -12,15 +12,15 @@ ------------------------------------------------------------------------- */ #include "imbalance_var.h" -#include -#include + #include "atom.h" +#include "error.h" #include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "variable.h" + +#include using namespace LAMMPS_NS; diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index 0c1a45603e3e09817b8ffb24e95d6b9b6a0258e9..431cc039974515af0c7e651ce0c41f5db089bc87 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_deprecated.h" -#include + #include "improper_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index ce0f36539fcfcf1c72a72c05d33c1f95c21755be..096e0c36142f8dc74d6d9265544dce82d74d24d5 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "improper_hybrid.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index f269f8bf030269c69b88be2c190bfd7aed1b7de4..3da38a890c34979ae8596c61d8932d822e402982 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "improper_zero.h" -#include + #include "atom.h" -#include "force.h" -#include "memory.h" #include "error.h" -#include "utils.h" +#include "memory.h" + +#include using namespace LAMMPS_NS; diff --git a/src/info.cpp b/src/info.cpp index fbe43442f0f84af4426da4223d10dd0a18ac98e2..87161e9ca5412f9d58b5f963599fc698f772a376 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -17,39 +17,37 @@ ------------------------------------------------------------------------- */ #include "info.h" -#include -#include -#include -#include -#include -#include -#include + #include "accelerator_kokkos.h" +#include "angle.h" #include "atom.h" +#include "bond.h" #include "comm.h" #include "compute.h" +#include "dihedral.h" #include "domain.h" #include "dump.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" -#include "improper.h" #include "group.h" +#include "improper.h" #include "input.h" #include "modify.h" #include "neighbor.h" #include "output.h" +#include "pair.h" +#include "pair_hybrid.h" #include "region.h" #include "universe.h" -#include "variable.h" #include "update.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "variable.h" + +#include +#include +#include +#include +#include #ifdef _WIN32 #define PSAPI_VERSION 1 @@ -105,6 +103,8 @@ static const int STYLES = ATOM_STYLES | INTEGRATE_STYLES | MINIMIZE_STYLES | DUMP_STYLES | COMMAND_STYLES; } +using namespace LAMMPS_NS; + static const char *varstyles[] = { "index", "loop", "world", "universe", "uloop", "string", "getenv", "file", "atomfile", "format", "equal", "atom", "vector", "python", "internal", "(unknown)"}; @@ -116,17 +116,15 @@ static const char *commlayout[] = { "uniform", "nonuniform", "irregular" }; static const char bstyles[] = "pfsm"; -using namespace LAMMPS_NS; -using namespace std; - template -static void print_columns(FILE* fp, map * styles); +static void print_columns(FILE *fp, std::map *styles); template -static bool find_style(const LAMMPS * lmp, map * styles, const string & name, bool suffix_check); +static bool find_style(const LAMMPS *lmp, std::map *styles, + const std::string &name, bool suffix_check); template -static vector get_style_names(map * styles); +static std::vector get_style_names(std::map *styles); /* ---------------------------------------------------------------------- */ @@ -357,7 +355,7 @@ void Info::command(int narg, char **arg) if (flags & COMM) { int major,minor; - string version = get_mpi_info(major,minor); + std::string version = get_mpi_info(major,minor); fmt::print(out,"\nCommunication information:\n" "MPI library level: MPI v{}.{}\n" @@ -949,7 +947,7 @@ bool Info::is_defined(const char *category, const char *name) return false; } -bool Info::has_style(const string & category, const string & name) +bool Info::has_style(const std::string &category, const std::string &name) { if ( category == "atom" ) { return find_style(lmp, atom->avec_map, name, false); @@ -983,7 +981,7 @@ bool Info::has_style(const string & category, const string & name) return false; } -vector Info::get_available_styles(const string & category) +std::vector Info::get_available_styles(const std::string &category) { if ( category == "atom" ) { return get_style_names(atom->avec_map); @@ -1014,13 +1012,13 @@ vector Info::get_available_styles(const string & category) } else if( category == "command" ) { return get_style_names(input->command_map); } - return vector(); + return std::vector(); } template -static vector get_style_names(map * styles) +static std::vector get_style_names(std::map *styles) { - vector names; + std::vector names; names.reserve(styles->size()); for(auto const& kv : *styles) { @@ -1033,7 +1031,8 @@ static vector get_style_names(map * styles) } template -static bool find_style(const LAMMPS* lmp, map * styles, const string & name, bool suffix_check) +static bool find_style(const LAMMPS *lmp, std::map *styles, + const std::string &name, bool suffix_check) { if (styles->find(name) != styles->end()) { return true; @@ -1041,13 +1040,13 @@ static bool find_style(const LAMMPS* lmp, map * styles, const if (suffix_check && lmp->suffix_enable) { if (lmp->suffix) { - string name_w_suffix = name + "/" + lmp->suffix; + std::string name_w_suffix = name + "/" + lmp->suffix; if (find_style(lmp, styles, name_w_suffix, false)) { return true; } } if (lmp->suffix2) { - string name_w_suffix = name + "/" + lmp->suffix2; + std::string name_w_suffix = name + "/" + lmp->suffix2; if (find_style(lmp, styles, name_w_suffix, false)) { return true; } @@ -1057,7 +1056,7 @@ static bool find_style(const LAMMPS* lmp, map * styles, const } template -static void print_columns(FILE* fp, map * styles) +static void print_columns(FILE *fp, std::map *styles) { if (styles->empty()) { fprintf(fp, "\nNone"); @@ -1066,8 +1065,8 @@ static void print_columns(FILE* fp, map * styles) // std::map keys are already sorted int pos = 80; - for(typename map::iterator it = styles->begin(); it != styles->end(); ++it) { - const string & style_name = it->first; + for(typename std::map::iterator it = styles->begin(); it != styles->end(); ++it) { + const std::string &style_name = it->first; // skip "secret" styles if (isupper(style_name[0])) continue; @@ -1149,9 +1148,9 @@ bool Info::has_package(const char * package_name) { /* ---------------------------------------------------------------------- */ #define _INFOBUF_SIZE 256 -string Info::get_os_info() +std::string Info::get_os_info() { - string buf; + std::string buf; #if defined(_WIN32) DWORD fullversion,majorv,minorv,buildv=0; @@ -1191,9 +1190,9 @@ string Info::get_os_info() return buf; } -string Info::get_compiler_info() +std::string Info::get_compiler_info() { - string buf; + std::string buf; #if __clang__ buf = fmt::format("Clang C++ {}", __VERSION__); #elif __INTEL_COMPILER @@ -1208,7 +1207,7 @@ string Info::get_compiler_info() return buf; } -string Info::get_openmp_info() +std::string Info::get_openmp_info() { #if !defined(_OPENMP) @@ -1243,7 +1242,7 @@ string Info::get_openmp_info() #endif } -string Info::get_mpi_vendor() { +std::string Info::get_mpi_vendor() { #if defined(MPI_STUBS) return "MPI STUBS"; #elif defined(OPEN_MPI) @@ -1263,7 +1262,7 @@ string Info::get_mpi_vendor() { #endif } -string Info::get_mpi_info(int &major, int &minor) +std::string Info::get_mpi_info(int &major, int &minor) { int len; #if (defined(MPI_VERSION) && (MPI_VERSION > 2)) || defined(MPI_STUBS) @@ -1279,10 +1278,10 @@ string Info::get_mpi_info(int &major, int &minor) char *ptr = strchr(version+80,'\n'); if (ptr) *ptr = '\0'; } - return string(version); + return std::string(version); } -string Info::get_cxx_info() +std::string Info::get_cxx_info() { #if __cplusplus > 201703L return "newer than C++17"; diff --git a/src/info.h b/src/info.h index 5a379eaa7845ba7c17527f9279a71a14cde53a89..65690ab28e27b13dabcaa207c5903ef0f2f281ed 100644 --- a/src/info.h +++ b/src/info.h @@ -21,7 +21,7 @@ CommandStyle(info,Info) #define LMP_INFO_H #include "pointers.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/input.cpp b/src/input.cpp index c74232648c7a635fabeba3b40b3430acff921f88..1cb789387107ac22280a38f7c559986e8bc8cd8c 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -12,45 +12,42 @@ ------------------------------------------------------------------------- */ #include "input.h" -#include -#include -#include -#include -#include -#include -#include -#include "style_command.h" -#include "universe.h" + +#include "accelerator_kokkos.h" +#include "angle.h" #include "atom.h" #include "atom_vec.h" +#include "bond.h" #include "comm.h" #include "comm_brick.h" #include "comm_tiled.h" -#include "group.h" -#include "domain.h" -#include "output.h" -#include "thermo.h" -#include "force.h" -#include "pair.h" -#include "min.h" -#include "modify.h" #include "compute.h" -#include "fix.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "update.h" +#include "memory.h" +#include "min.h" +#include "modify.h" #include "neighbor.h" +#include "output.h" +#include "pair.h" #include "special.h" +#include "style_command.h" +#include "thermo.h" #include "timer.h" +#include "universe.h" +#include "update.h" #include "variable.h" -#include "accelerator_kokkos.h" -#include "error.h" -#include "memory.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include +#include +#include #ifdef _WIN32 #include diff --git a/src/input.h b/src/input.h index 48caa13fde0ddad50f5d61b74c689a57775dca9e..b8ffb276f9a834d1843eb0712be7eabcadd62ae8 100644 --- a/src/input.h +++ b/src/input.h @@ -15,8 +15,8 @@ #define LMP_INPUT_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/irregular.cpp b/src/irregular.cpp index 2213b37d55d35d4d77b07fa38f49132a9f604a14..f6de6947bd8eec0fce1514a0434c888ccc26e90c 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "irregular.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" -#include "modify.h" +#include "domain.h" #include "fix.h" #include "memory.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; diff --git a/src/kspace.cpp b/src/kspace.cpp index 2485db67b87bd8522559ba8492884becd6ad573a..e51cc54c973a3e8e4d86c5a54e52466e7d36aad0 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -12,21 +12,19 @@ ------------------------------------------------------------------------- */ #include "kspace.h" -#include -#include -#include -#include -#include + #include "atom.h" +#include "atom_masks.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" -#include "pair.h" #include "memory.h" -#include "atom_masks.h" -#include "error.h" +#include "pair.h" #include "suffix.h" -#include "domain.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/kspace_deprecated.cpp b/src/kspace_deprecated.cpp index 5dc2b50e2be091c29a7b487e1318fe5fa6912f09..16e9ff6abb037e722be651894332b0129ee8b42a 100644 --- a/src/kspace_deprecated.cpp +++ b/src/kspace_deprecated.cpp @@ -16,11 +16,10 @@ ------------------------------------------------------------------------- */ #include "kspace_deprecated.h" -#include + #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" using namespace LAMMPS_NS; diff --git a/src/lammps.cpp b/src/lammps.cpp index ded9d93167eed6ce244b0850948546e41da759e9..4d643c327cb43006243d719d17bf63867c039f00 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -12,13 +12,7 @@ ------------------------------------------------------------------------- */ #include "lammps.h" -#include -#include -#include -#include -#include -#include -#include + #include "style_angle.h" // IWYU pragma: keep #include "style_atom.h" // IWYU pragma: keep #include "style_bond.h" // IWYU pragma: keep @@ -36,12 +30,12 @@ #include "universe.h" #include "input.h" #include "info.h" -#include "atom.h" +#include "atom.h" // IWYU pragma: keep #include "update.h" -#include "neighbor.h" +#include "neighbor.h" // IWYU pragma: keep #include "comm.h" #include "comm_brick.h" -#include "domain.h" +#include "domain.h" // IWYU pragma: keep #include "force.h" #include "modify.h" #include "group.h" @@ -54,8 +48,11 @@ #include "version.h" #include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include +#include #include "lmpinstalledpkgs.h" #include "lmpgitversion.h" diff --git a/src/lattice.cpp b/src/lattice.cpp index f41c32d2394981a1950a73dfc66b05dd2ba1c040..68f3e7abe12050ab4eeee7f95beb9cb924c80049 100644 --- a/src/lattice.cpp +++ b/src/lattice.cpp @@ -12,17 +12,15 @@ ------------------------------------------------------------------------- */ #include "lattice.h" -#include -#include -#include -#include "update.h" -#include "domain.h" + #include "comm.h" -#include "force.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "memory.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/library.cpp b/src/library.cpp index 30d52aefe5b0d3622ce2e1bd670a120d9d25833e..3f37aecd7a1316c34e5d9bce05b80fdf9bfc4faa 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -16,33 +16,31 @@ #include "library.h" #include -#include -#include -#include -#include -#include "universe.h" -#include "atom_vec.h" + #include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "compute.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "fix.h" +#include "fix_external.h" +#include "force.h" #include "group.h" +#include "info.h" #include "input.h" -#include "variable.h" +#include "memory.h" #include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" #include "output.h" #include "thermo.h" -#include "compute.h" -#include "fix.h" -#include "comm.h" -#include "memory.h" -#include "error.h" -#include "force.h" -#include "info.h" -#include "fix_external.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" diff --git a/src/lmptype.h b/src/lmptype.h index e2e7a88a42d4cfb366762ea548b9a8f0d2344f0d..e0e081dd129abdc1d0fe2e90a0449cc997748c51 100644 --- a/src/lmptype.h +++ b/src/lmptype.h @@ -42,10 +42,10 @@ #define __STDC_FORMAT_MACROS #endif -#include -#include -#include -#include +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export // grrr - IBM Power6 does not provide this def in their system header files diff --git a/src/main.cpp b/src/main.cpp index 9fb084aaea681aec5b003c82dccc3851197f0ab7..d705db4e5bda55631a1d3507fadf7ddb709f5e17 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -12,9 +12,11 @@ ------------------------------------------------------------------------- */ #include "lammps.h" -#include #include "input.h" +#include +#include + #if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE) #include #endif diff --git a/src/memory.cpp b/src/memory.cpp index 6211687a7af6e6b7c159c01166a33b1a51a770ca..bbbc233bbf81b5eef5bff16ae398f984eb7e28f2 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -12,9 +12,8 @@ ------------------------------------------------------------------------- */ #include "memory.h" -#include + #include "error.h" -#include "fmt/format.h" #if defined(LMP_USER_INTEL) && defined(__INTEL_COMPILER) #ifndef LMP_INTEL_NO_TBB diff --git a/src/min.cpp b/src/min.cpp index 0bf04455258436f3ee896f97834ba9247ae39347..6bcb4b4e2e1e11f17b6e4b26c0bf91a1aee1ef37 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -20,32 +20,32 @@ ------------------------------------------------------------------------- */ #include "min.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" -#include "fix_minimize.h" #include "compute.h" -#include "neighbor.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix_minimize.h" +#include "force.h" #include "improper.h" #include "kspace.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" #include "timer.h" -#include "math_const.h" -#include "memory.h" -#include "error.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/min.h b/src/min.h index b23c9b66700bcecc4c4d82f1b6ca89004f1c92d8..1db196a55e8e69331645b50ac493175573b0ed16 100644 --- a/src/min.h +++ b/src/min.h @@ -14,7 +14,7 @@ #ifndef LMP_MIN_H #define LMP_MIN_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/min_cg.cpp b/src/min_cg.cpp index 46da4bfa5ba5cea9c77f224f33202dde39fb3bea..511b16cef86144f3c726d80fe3bca6f98cb91145 100644 --- a/src/min_cg.cpp +++ b/src/min_cg.cpp @@ -12,12 +12,13 @@ ------------------------------------------------------------------------- */ #include "min_cg.h" -#include -#include + #include "error.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_fire.cpp b/src/min_fire.cpp index 53bedfbb6c2ae9570082884da17068378915061e..b7225a1a5a47876c4fa59ccbbad60eaa52f9c007 100644 --- a/src/min_fire.cpp +++ b/src/min_fire.cpp @@ -16,21 +16,18 @@ Erik Bitzek, FAU Erlangen-Nuernberg ------------------------------------------------------------------------- */ -#include #include "min_fire.h" -#include "universe.h" + #include "atom.h" +#include "comm.h" +#include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" -#include "error.h" -#include "variable.h" -#include "modify.h" -#include "compute.h" -#include "domain.h" -#include "neighbor.h" -#include "comm.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_fire_old.cpp b/src/min_fire_old.cpp index bd76b2d1fcafce45e89b047e24f7a4efaa129423..6efd00a4b85902f5af3e18b34fde2ab47bf8de54 100644 --- a/src/min_fire_old.cpp +++ b/src/min_fire_old.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "min_fire_old.h" -#include -#include -#include "universe.h" + #include "atom.h" #include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp index 63432aab63593c3c0499f65226d7ce787c4707c7..909f0b0689cfc4c74a0a3726dbab770b2f4c5991 100644 --- a/src/min_hftn.cpp +++ b/src/min_hftn.cpp @@ -18,17 +18,18 @@ ------------------------------------------------------------------------- */ #include "min_hftn.h" -#include -#include -#include + #include "atom.h" #include "error.h" #include "fix_minimize.h" #include "modify.h" #include "output.h" #include "pair.h" -#include "update.h" #include "timer.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp index a7a10dcd5172fd39e49e300906b6c59e01964a7d..7226f616147deb4d811d321a47831ac665b2a55b 100644 --- a/src/min_linesearch.cpp +++ b/src/min_linesearch.cpp @@ -22,15 +22,16 @@ ------------------------------------------------------------------------- */ #include "min_linesearch.h" -#include -#include + #include "atom.h" -#include "modify.h" #include "fix_minimize.h" -#include "pair.h" +#include "modify.h" #include "output.h" +#include "pair.h" #include "thermo.h" +#include + using namespace LAMMPS_NS; // ALPHA_MAX = max alpha allowed to avoid long backtracks diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp index 5e7643bf3be0796118494a80147e1020822d93f6..025e80b95db0c667b4b9eb5915936d35665bd023 100644 --- a/src/min_quickmin.cpp +++ b/src/min_quickmin.cpp @@ -12,15 +12,16 @@ ------------------------------------------------------------------------- */ #include "min_quickmin.h" -#include -#include -#include "universe.h" + #include "atom.h" #include "error.h" #include "force.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/min_sd.cpp b/src/min_sd.cpp index d973ec1c8267410a0aed4aa38165591bf5bee092..5868acbe48c9641e9492a1772679d3f3c00a2d47 100644 --- a/src/min_sd.cpp +++ b/src/min_sd.cpp @@ -12,11 +12,13 @@ ------------------------------------------------------------------------- */ #include "min_sd.h" -#include + #include "error.h" -#include "update.h" #include "output.h" #include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/minimize.cpp b/src/minimize.cpp index 01463907635418cc1dabedfe6f156d74857e5ee6..451412ecc8a8dc7d14c9a08cfc3aaf1df282af76 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "minimize.h" + #include "domain.h" -#include "update.h" -#include "min.h" +#include "error.h" #include "finish.h" +#include "min.h" #include "timer.h" -#include "error.h" -#include "force.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/modify.cpp b/src/modify.cpp index 96335946ae6abbd0b5e0109fda3a05ff6a4d45c0..c88d52b6237573234de7004cb01904da81358f96 100644 --- a/src/modify.cpp +++ b/src/modify.cpp @@ -12,24 +12,24 @@ ------------------------------------------------------------------------- */ #include "modify.h" -#include -#include #include "style_compute.h" #include "style_fix.h" + #include "atom.h" #include "comm.h" -#include "fix.h" #include "compute.h" -#include "group.h" -#include "update.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "fix.h" +#include "group.h" #include "input.h" -#include "variable.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "region.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -947,7 +947,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix) void Modify::add_fix(const std::string &fixcmd, int trysuffix) { - std::vector args = utils::split_words(fixcmd); + auto args = utils::split_words(fixcmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { @@ -1249,7 +1249,7 @@ void Modify::add_compute(int narg, char **arg, int trysuffix) void Modify::add_compute(const std::string &computecmd, int trysuffix) { - std::vector args = utils::split_words(computecmd); + auto args = utils::split_words(computecmd); char **newarg = new char*[args.size()]; int i=0; for (const auto &arg : args) { diff --git a/src/modify.h b/src/modify.h index 05eebc7e141c3bef2ae38238756eeb63c2dbdb05..4c3db0a1b9fb9412c2b115c148d199d65d7dcfc4 100644 --- a/src/modify.h +++ b/src/modify.h @@ -15,11 +15,14 @@ #define LMP_MODIFY_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { + class Compute; + class Fix; + class Modify : protected Pointers { friend class Info; friend class FixSRP; @@ -27,7 +30,6 @@ class Modify : protected Pointers { friend class RespaOMP; public: - int nfix,maxfix; int n_initial_integrate,n_post_integrate,n_pre_exchange; int n_pre_neighbor,n_post_neighbor; int n_pre_force,n_pre_reverse,n_post_force; @@ -41,11 +43,12 @@ class Modify : protected Pointers { int nfix_restart_global; // stored fix global info from restart file int nfix_restart_peratom; // stored fix peratom info from restart file - class Fix **fix; // list of fixes + int nfix,maxfix; + Fix **fix; // list of fixes int *fmask; // bit mask for when each fix is applied - int ncompute,maxcompute; // list of computes - class Compute **compute; + int ncompute,maxcompute; + Compute **compute; // list of computes Modify(class LAMMPS *); virtual ~Modify(); diff --git a/src/molecule.cpp b/src/molecule.cpp index 18f5c389928d5fe64cfdb069669229940d12bb04..0d81f49a5083c9af3288dd1c37743b4c579ba2d1 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -12,23 +12,22 @@ ------------------------------------------------------------------------- */ #include "molecule.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" #include "atom_vec_body.h" -#include "force.h" #include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_extra.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" #include "tokenizer.h" +#include +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 256 diff --git a/src/molecule.h b/src/molecule.h index d752be3f81bdd8fccb59643b738dc25f2b6e7588..5a3fa5a32764e0f58a81f62c5975d46dc48636d7 100644 --- a/src/molecule.h +++ b/src/molecule.h @@ -15,7 +15,7 @@ #define LMP_ONE_MOLECULE_H #include "pointers.h" -#include + #include namespace LAMMPS_NS { diff --git a/src/neigh_list.h b/src/neigh_list.h index 501188a72439a9ec3f317ef27de3632dfb86507c..c26b00813634d78afdcc95173c9827d45257e60c 100644 --- a/src/neigh_list.h +++ b/src/neigh_list.h @@ -14,7 +14,7 @@ #ifndef LMP_NEIGH_LIST_H #define LMP_NEIGH_LIST_H -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/neighbor.cpp b/src/neighbor.cpp index c9b16f67a0fb7f7299b84d3922bca9a5ddb900ea..66ab92496ae0e57dc557b72308c401885c63ec50 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -16,38 +16,37 @@ ------------------------------------------------------------------------- */ #include "neighbor.h" -#include -#include -#include + +#include "atom.h" +#include "atom_vec.h" +#include "citeme.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "memory.h" +#include "modify.h" +#include "nbin.h" #include "neigh_list.h" #include "neigh_request.h" -#include "nbin.h" -#include "nstencil.h" #include "npair.h" +#include "nstencil.h" #include "ntopo.h" +#include "output.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "respa.h" #include "style_nbin.h" -#include "style_nstencil.h" #include "style_npair.h" +#include "style_nstencil.h" #include "style_ntopo.h" -#include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "force.h" -#include "pair.h" -#include "pair_hybrid.h" -#include "domain.h" -#include "group.h" -#include "modify.h" -#include "fix.h" -#include "compute.h" #include "update.h" -#include "respa.h" -#include "output.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include using namespace LAMMPS_NS; using namespace NeighConst; diff --git a/src/ntopo.cpp b/src/ntopo.cpp index ca63b8532818f102ae0699c64d76f7edc5bb6cb5..d4ddcc7fc0528a6a7d3b0142943b14328fb77196 100644 --- a/src/ntopo.cpp +++ b/src/ntopo.cpp @@ -12,13 +12,13 @@ ------------------------------------------------------------------------- */ #include "ntopo.h" -#include + #include "atom.h" -#include "neighbor.h" #include "comm.h" #include "domain.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "neighbor.h" using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp index 71521e6891b33bdc74e588dec1212c8a8180e2a9..21ac894d92668d498f54c32c61e2d72940150707 100644 --- a/src/ntopo_angle_all.cpp +++ b/src/ntopo_angle_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp index c72073718e409332421bc16e2c15c98c41bf611b..583339ed110c1be86be3b7fbd1aec7f0b4775b50 100644 --- a/src/ntopo_angle_partial.cpp +++ b/src/ntopo_angle_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp index d6303a0ad4d4f08a476ce5408f0ee4844911a46a..17e17ca462d6a61b8b7706968df51522dbd52bc2 100644 --- a/src/ntopo_angle_template.cpp +++ b/src/ntopo_angle_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_angle_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp index 9fac01bdba2f7aa5100b83979b855fb5b19f6909..20ec5aa290c39dc24d6da63895fe4d1e57aa6a62 100644 --- a/src/ntopo_bond_all.cpp +++ b/src/ntopo_bond_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp index 138f8f4330ec252d80f6b4e3f44067bff7564283..9b5914b2c83165212872372ca9167d85763b11fa 100644 --- a/src/ntopo_bond_partial.cpp +++ b/src/ntopo_bond_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp index a651715320f639f1943cd4917e35635b20c6faa1..88a31460d9cee01d46b19c603868299756115016 100644 --- a/src/ntopo_bond_template.cpp +++ b/src/ntopo_bond_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_bond_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp index 81193605c1d37c99eb744b075eb268cd0643c1ec..bcfe8ce712080e63d21524faa74fcbe0ee51041d 100644 --- a/src/ntopo_dihedral_all.cpp +++ b/src/ntopo_dihedral_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp index 855fa800b620ad2ffcbb62e9ac03814de4f8fd2d..31a78c5c4828d0904d4e1a999b68b2f34358ee13 100644 --- a/src/ntopo_dihedral_partial.cpp +++ b/src/ntopo_dihedral_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp index 06fac504000a1a4019e749c3107121f495d43d07..0d2a9451e095ebae868f1ad2d696f6095408995a 100644 --- a/src/ntopo_dihedral_template.cpp +++ b/src/ntopo_dihedral_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_dihedral_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp index e839e9161b119cb2f984ae2ff708c070e1161901..53f229a86a01e66e3b47cf8c9f3c4c5ca5265893 100644 --- a/src/ntopo_improper_all.cpp +++ b/src/ntopo_improper_all.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_all.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp index c4c6ec317712178f4f120bd4772345ae4aca865a..8fc619c9e48723c3e6f98e33c7e2f49a29438fa0 100644 --- a/src/ntopo_improper_partial.cpp +++ b/src/ntopo_improper_partial.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_partial.h" -#include + #include "atom.h" #include "force.h" #include "domain.h" @@ -21,7 +21,7 @@ #include "thermo.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp index 060ba173fddba22fa17dfb7b993ef3f1d07a2b01..bd19d5877ccde700cf4fbc54e225a888713799df 100644 --- a/src/ntopo_improper_template.cpp +++ b/src/ntopo_improper_template.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "ntopo_improper_template.h" -#include + #include "atom.h" #include "atom_vec.h" #include "force.h" @@ -23,7 +23,7 @@ #include "molecule.h" #include "memory.h" #include "error.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/output.cpp b/src/output.cpp index 16d2fa54a0e710d46dc14b7229c527567ee61f4e..6c90198de4da3a81efb1dec223da0a794a1cf722 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -12,27 +12,25 @@ ------------------------------------------------------------------------- */ #include "output.h" -#include -#include -#include -#include "style_dump.h" +#include "style_dump.h" // IWYU pragma: keep + #include "atom.h" -#include "neighbor.h" -#include "input.h" -#include "variable.h" #include "comm.h" -#include "update.h" -#include "group.h" #include "domain.h" -#include "thermo.h" -#include "modify.h" -#include "force.h" #include "dump.h" -#include "write_restart.h" -#include "memory.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "thermo.h" +#include "update.h" +#include "variable.h" +#include "write_restart.h" + +#include using namespace LAMMPS_NS; @@ -81,7 +79,7 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp) #define DUMP_CLASS #define DumpStyle(key,Class) \ (*dump_map)[#key] = &dump_creator; -#include "style_dump.h" +#include "style_dump.h" // IWYU pragma: keep #undef DumpStyle #undef DUMP_CLASS } diff --git a/src/output.h b/src/output.h index 1bf4128ee0f190609518500a36ec3629b602f9fb..06be7b244a8c2535d72e687e5a70182841ec6efc 100644 --- a/src/output.h +++ b/src/output.h @@ -15,11 +15,13 @@ #define LMP_OUTPUT_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { +class Dump; + class Output : protected Pointers { public: bigint next; // next timestep for any kind of output @@ -39,7 +41,7 @@ class Output : protected Pointers { bigint *last_dump; // last timestep each snapshot was output char **var_dump; // variable name for dump frequency int *ivar_dump; // variable index for dump frequency - class Dump **dump; // list of defined Dumps + Dump **dump; // list of defined Dumps int restart_flag; // 1 if any restart files are written int restart_flag_single; // 1 if single restart files are written diff --git a/src/pair.cpp b/src/pair.cpp index e003ef740ac1d9fe9bb95026c2890c61c580d330..d869bbe8d8e98bd64c47f0692aa6e3edc77c9d43 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -16,28 +16,26 @@ ------------------------------------------------------------------------- */ #include "pair.h" -#include -#include // IWYU pragma: keep -#include // IWYU pragma: keep -#include -#include -#include -#include + #include "atom.h" -#include "neighbor.h" -#include "domain.h" +#include "atom_masks.h" #include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "compute.h" -#include "suffix.h" -#include "atom_masks.h" -#include "memory.h" #include "math_const.h" -#include "error.h" +#include "memory.h" +#include "neighbor.h" +#include "suffix.h" #include "update.h" -#include "utils.h" -#include "fmt/format.h" + +#include // IWYU pragma: keep +#include // IWYU pragma: keep +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index a858f8791065662eb5febca85deeb86cd0fb71f4..87aa0bab5f2dc69380623b0cdedad775907d25d6 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_beck.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathSpecial; diff --git a/src/pair_born.cpp b/src/pair_born.cpp index ca0ab9a17b997288d1f906d4801a0231bff0513c..5b0d3a656210af8b078da355f4eafe33b45822fd 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_born.h" -#include + #include #include #include "atom.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index 1a6b12a3458f9ed442495b8d8e138ea8c491879d..e4617b5c4b847d0a70c6b95bd9fb6ac5d6c454bc 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_dsf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "error.h" #include "math_special.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 4c51b0bb9f09b6bdb28acac7be96ee67a5e1be30..30fe8fcde9021d542857509782d347df715ff71c 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_born_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 91071fccb1c5050905deafdd7245a0253b80b424..1abdbcc68bd618011bb6b41dddd040bc1a181e37 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 6141205db051bd36da6ad6fb52f6852f2787f257..9fac17aede4e9a2a8dfa68d6627cb5df9781568a 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_buck_coul_cut.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index d19374b5d9b167d3a7ceaf4f6a4e755bd15c2ee4..67c471a5e3e52f665e859286f14add67ec5beee7 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_cut.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 2a3def0d4f20830a287b07ad009af375c3bf4e34..20937182455d6dfbc28f0ad27284c1c6a04e11d4 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_coul_debye.h" -#include + #include #include "atom.h" #include "comm.h" #include "force.h" #include "neigh_list.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 2f1a834060f53c4934603f45d44aa25420aae2c3..ee124c7f59f500dfa83652c88ec9f7acd2faedbf 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_dsf.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index efe8d460177a3bd4f5404476ac8662aab73bb800..e538275b3ca3fd1b4bcaf65964ca8ce273c463d7 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -16,23 +16,22 @@ ------------------------------------------------------------------------- */ #include "pair_coul_streitz.h" -#include -#include -#include -#include + #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "potential_file_reader.h" +#include "tokenizer.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index e94c4abb73bedf3ab3801c395e4f3109819bada4..e3079dcaf659e8c6e77d1e62625e134e75d7452b 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 75cb7efcdf96ed61d245357b757ca9251486da5f..046726892e318d59210a19441678bb4cae74c1a6 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -16,12 +16,12 @@ ------------------------------------------------------------------------- */ #include "pair_deprecated.h" -#include + #include "pair_hybrid.h" #include "comm.h" #include "force.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 613ad90cc39986c413bdfc2c4d0edeef6283c7dd..d0d9b98fc9f4bbd60eac9ad20c8cd46e065f9c92 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd.h" -#include + #include #include "atom.h" #include "comm.h" @@ -27,7 +27,7 @@ #include "random_mars.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index 3f3f05f7f5a6fed85100698aa0aa6922539aed69..dd0e144953a4b15650cf7bfa970ccefcece2be4a 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_dpd_tstat.h" -#include + #include #include "atom.h" #include "update.h" @@ -21,7 +21,7 @@ #include "comm.h" #include "random_mars.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index d8b8e36b8c1c012c5486e77c84cab61fea861daf..67322967641dc952d98d4a4a6686d4f079264555 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_gauss.h" -#include + #include #include #include "atom.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 693ed7fa243d6e4f961936f8b699119df45e64a6..0b1882f12be0d299df7beb772fd0c413640d1d5a 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -13,7 +13,7 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid.h" -#include + #include #include #include "atom.h" @@ -26,9 +26,9 @@ #include "memory.h" #include "error.h" #include "respa.h" -#include "utils.h" + #include "suffix.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp index dc8ac65dd44edd966d4847a0410dc816c8970f84..34c4cfe41864e7d7fdbd808beb1623c30dafce9f 100644 --- a/src/pair_hybrid_overlay.cpp +++ b/src/pair_hybrid_overlay.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "pair_hybrid_overlay.h" -#include -#include + #include "atom.h" -#include "force.h" #include "error.h" -#include "utils.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index c60908e8cf9cac203388536e4639bf9c795db3d0..a4ba3b858517e66152c229d6ea17c3f9555017d8 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj96_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 833c9543305192a5ce39a5486e82bc3205795de2..b6c91cafe205d15a12af7283f60cba098da54477 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cubic.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace PairLJCubicConstants; diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index fedf029fb85cc0e7cd1393f0b6971056c8c4f270..bd42801f3b1c3e77d5095b594ccada83256594f2 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index a11de35c537a68ca110b01d30865b7656b210d2c..669d48c86090ac159b82d19d34cf891c303e68c4 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_cut.h" -#include + #include #include #include "atom.h" @@ -23,7 +23,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index 2d4b0bbe98da21c8dc3f5d71a7b05e94b783f8ca..3ddb898c8feeb7e65599b7e1f61c4e2450958f18 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_debye.h" -#include + #include #include "atom.h" #include "neigh_list.h" #include "force.h" #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index 2d9368a0cafcb1960fe3c351d9e5dfd3bc347f66..952a140039db532bee480a57840019f03f27d8c0 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -17,7 +17,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_dsf.h" -#include + #include #include #include "atom.h" @@ -28,7 +28,7 @@ #include "memory.h" #include "math_const.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index c6fa33f03c141ddd1638ce80ab587a2f7921a85e..749cc9e6a952cbbaff5b1818d455ea5ffe330733 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_cut_coul_wolf.h" -#include + #include #include "atom.h" #include "comm.h" @@ -26,7 +26,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 1063d056721836fe94067eba9bd6f09f88ffe46d..3f711e2a159b700d04b7dcdd738e68050ba51884 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_expand.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index b7e3516ec3b2590c16d64e311dcd7fefdff53212..0818c60f315caadf640bfbd66f75e03df1250021 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 37837b695f1cf0c1bc67d98c608cf6e07a8d6ac1..005bc44061d3a4a591f0bbfeb1674e723ede817f 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_gromacs_coul_gromacs.h" -#include + #include #include "atom.h" #include "comm.h" @@ -25,7 +25,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index 5c6bc671f910490c8c278c20a0b90486cda23f8b..a53d703b8bbe7fb67f35cdac5958b9a6612750ae 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 14646f19f27bd819cdbea098bf8871d002cf82f3..3697208d42bf7358b36161b32afa568a9cd054e3 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_lj_smooth_linear.h" -#include + #include #include "atom.h" #include "comm.h" @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index f838d961454a1efcd6e66d70cc839681a7f11aa6..7447e143f7de53a33462fae644378c0f64d72efa 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include "pair_mie_cut.h" -#include + #include #include #include "atom.h" @@ -30,7 +30,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index cbfaccab2ce0b6edb57c2b995e3e6146e626fdc4..efcc1aa81182d476a54b16750fcb64a166f9a92b 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_morse.h" -#include + #include #include #include "atom.h" @@ -21,7 +21,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index 4d3702313e952e70f4efdec10f9a526adc171de2..f3dd139b694ddfb15095d3ce7d6f66d016312c7e 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_soft.h" -#include + #include #include #include "atom.h" @@ -22,7 +22,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 4aec954c38efe0b90257d9b992e06fe0a42d6cc4..1711465ffa551d72217c791eeb571ac05a4f76cd 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -16,21 +16,21 @@ ------------------------------------------------------------------------- */ #include "pair_table.h" -#include + #include -#include + #include -#include + #include "atom.h" #include "force.h" #include "comm.h" #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + #include "tokenizer.h" #include "table_file_reader.h" -#include "fmt/format.h" + using namespace LAMMPS_NS; diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index fd700e98862ec0c145e76f0922ee57dd52fa72f2..50cc87cf96234afc18b2a4acfaa03955e95a0f2d 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -18,7 +18,7 @@ ------------------------------------------------------------------------- */ #include "pair_ufm.h" -#include + #include #include #include "atom.h" @@ -27,7 +27,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index b746204892105cd1541bbb2bc3b46dfdf61292f2..64294923462a9807620f3c362d431b5d2d28c7ef 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ #include "pair_yukawa.h" -#include + #include #include "atom.h" #include "force.h" @@ -20,7 +20,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index d78c1569359b014f15b41b854be348348ed7b5b8..68c63c98060e8bab8f84cd425871fe757a00c4b4 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -24,7 +24,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" -#include "utils.h" + // From J.F. Zeigler, J. P. Biersack and U. Littmark, // "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985. diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index f08d919f83eb1464461896ee4de5ff21c211fc91..976bb1ba332db7aa7e4c9ee9cb02df23ce07fb91 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -16,14 +16,13 @@ ------------------------------------------------------------------------- */ #include "pair_zero.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" #include "memory.h" #include "error.h" -#include "utils.h" + +#include using namespace LAMMPS_NS; diff --git a/src/pointers.h b/src/pointers.h index 4b91e009ac63865924139d30af3b4304bc730fc8..04f682f04504574286fc076a345e3c7537edb6c2 100644 --- a/src/pointers.h +++ b/src/pointers.h @@ -21,13 +21,14 @@ #ifndef LMP_POINTERS_H #define LMP_POINTERS_H -#include "lmptype.h" // IWYU pragma: export -#include // IWYU pragma: export -#include // IWYU pragme: export -#include // IWYU pragma: export -#include // IWYU pragma: export -#include "lammps.h" // IWYU pragma: export -#include "utils.h" // IWYU pragma: export +#include "lmptype.h" // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragme: export +#include // IWYU pragma: export +#include // IWYU pragma: export +#include "lammps.h" // IWYU pragma: export +#include "utils.h" // IWYU pragma: export +#include "fmt/format.h" // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index 62658a9ac5a5ba7d89f2d1cd73cf47bdeea1ab19..a71d7944d6fd3b3a9121ab7ba3a3b5fb4b9fdf08 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -15,17 +15,13 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "force.h" -#include "error.h" -#include "comm.h" #include "potential_file_reader.h" -#include "update.h" -#include "utils.h" -#include "tokenizer.h" -#include "fmt/format.h" -#include +#include "comm.h" +#include "error.h" +#include "text_file_reader.h" +#include "tokenizer.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/potential_file_reader.h b/src/potential_file_reader.h index 9094d3957a64a56cb4c81484333b1e4894236fec..d3befca282b00971de740041990bc7ad64c9d8fa 100644 --- a/src/potential_file_reader.h +++ b/src/potential_file_reader.h @@ -18,14 +18,13 @@ #ifndef LMP_POTENTIAL_FILE_READER_H #define LMP_POTENTIAL_FILE_READER_H -#include - -#include "pointers.h" +#include "pointers.h" // IWYU pragma: export #include "tokenizer.h" -#include "text_file_reader.h" namespace LAMMPS_NS { + class TextFileReader; + class PotentialFileReader : protected Pointers { protected: TextFileReader *reader; diff --git a/src/procmap.cpp b/src/procmap.cpp index 1741e351fe12a2fc9d79b62235cad5ecfc909647..f80af9330eeae4269a04caef17e9ee58f57b32e7 100644 --- a/src/procmap.cpp +++ b/src/procmap.cpp @@ -16,18 +16,18 @@ ------------------------------------------------------------------------- */ #include "procmap.h" -#include -#include -#include -#include -#include -#include -#include "universe.h" + #include "comm.h" #include "domain.h" +#include "error.h" #include "math_extra.h" #include "memory.h" -#include "error.h" +#include "universe.h" + +#include +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/rcb.cpp b/src/rcb.cpp index 2cc70a2de9530730a48e23228b7a07e902752f42..03c99560b30dd4f94c565d53696a79ecf3004e29 100644 --- a/src/rcb.cpp +++ b/src/rcb.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "rcb.h" -#include -#include + #include "irregular.h" #include "memory.h" +#include + using namespace LAMMPS_NS; #define MYHUGE 1.0e30 diff --git a/src/read_data.cpp b/src/read_data.cpp index 7224ac89ea1ec9581886e5b438e1a7f82b7b2474..2a6801b3a578c9c5d4659f1f1db364e37fd6c530 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -16,34 +16,32 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_data.h" -#include -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "molecule.h" -#include "group.h" +#include "bond.h" #include "comm.h" -#include "update.h" -#include "modify.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "force.h" -#include "pair.h" -#include "domain.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" -#include "special.h" #include "irregular.h" -#include "error.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "molecule.h" +#include "pair.h" +#include "special.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/read_dump.cpp b/src/read_dump.cpp index fbafb4ca8482b9924b3d35ba17ad51bd4fd203c5..10218fe61707a1e93b0e55bb464882ea9de5db07 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -20,22 +20,19 @@ // before lmptype.h can set flags to insure it is done correctly #include "read_dump.h" -#include -#include -#include -#include "reader.h" -#include "style_reader.h" + #include "atom.h" #include "atom_vec.h" -#include "update.h" -#include "domain.h" #include "comm.h" -#include "force.h" -#include "irregular.h" +#include "domain.h" #include "error.h" +#include "irregular.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "reader.h" +#include "style_reader.h" // IWYU pragma: keep +#include "update.h" + +#include using namespace LAMMPS_NS; @@ -246,7 +243,7 @@ void ReadDump::setup_reader(int narg, char **arg) for (int i = 0; i < nreader; i++) \ readers[i] = new Class(lmp); \ } -#include "style_reader.h" +#include "style_reader.h" // IWYU pragma: keep #undef READER_CLASS // unrecognized style diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 157992bce3b593da129b27d235e794334961a434..dcab9f834c4fcd11f5a1b40ee1bb322163b7c7ba 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -12,31 +12,30 @@ ------------------------------------------------------------------------- */ #include "read_restart.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" +#include "bond.h" #include "comm.h" -#include "irregular.h" -#include "update.h" -#include "modify.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix_read_restart.h" -#include "group.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" +#include "irregular.h" +#include "memory.h" +#include "modify.h" +#include "mpiio.h" +#include "pair.h" #include "special.h" #include "universe.h" -#include "mpiio.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "update.h" + +#include +#include #include "lmprestart.h" diff --git a/src/reader.cpp b/src/reader.cpp index 2a6e4bf90caca508ea6f4156ea7e7aaa5a655a1c..8230fa3ed306f452a8a887e86593594e28701586 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "reader.h" -#include + #include "error.h" -#include "utils.h" -#include "fmt/format.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reader_native.cpp b/src/reader_native.cpp index 9b93c7800000179a78b261f2a81a9cc14ba2f9ae..e0f0d7792b3d41b815d456c5050f762fc7387490 100644 --- a/src/reader_native.cpp +++ b/src/reader_native.cpp @@ -12,14 +12,14 @@ ------------------------------------------------------------------------- */ #include "reader_native.h" -#include -#include -#include "atom.h" -#include "memory.h" + #include "error.h" -#include "utils.h" +#include "memory.h" #include "tokenizer.h" +#include +#include + using namespace LAMMPS_NS; #define MAXLINE 1024 // max line length in dump file diff --git a/src/reader_native.h b/src/reader_native.h index 6456dc275ae3eb44e8e96b2c21bb74e8fb20fa92..d1c84330165260e229efcc1e54ab767e6a728a96 100644 --- a/src/reader_native.h +++ b/src/reader_native.h @@ -23,9 +23,8 @@ ReaderStyle(native,ReaderNative) #define LMP_READER_NATIVE_H #include "reader.h" -#include + #include -#include namespace LAMMPS_NS { diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp index ad8cb0cc6ea78f4f8ee90dc7ed3f839cffbdbeba..8a2f7a39891e077e723b771c843ab66844fd8cbe 100644 --- a/src/reader_xyz.cpp +++ b/src/reader_xyz.cpp @@ -16,10 +16,9 @@ ------------------------------------------------------------------------- */ #include "reader_xyz.h" -#include + #include "memory.h" #include "error.h" -#include "force.h" using namespace LAMMPS_NS; diff --git a/src/region.cpp b/src/region.cpp index 8a6ec3305aab77b979d036ce5439d9bec0de70c2..15b6fee27212768af60b6234440950f174c1ef50 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -12,16 +12,17 @@ ------------------------------------------------------------------------- */ #include "region.h" -#include -#include -#include "update.h" + #include "domain.h" -#include "lattice.h" +#include "error.h" #include "input.h" -#include "variable.h" +#include "lattice.h" #include "math_extra.h" -#include "error.h" -#include "force.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_block.cpp b/src/region_block.cpp index e06c05d1a714d0d9a32fe09f6108bc541b3619db..2204f2e6a474cc0dc378ab0631457f5a73ee04bd 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -12,11 +12,12 @@ ------------------------------------------------------------------------- */ #include "region_block.h" -#include -#include "force.h" + #include "domain.h" -#include "math_extra.h" #include "error.h" +#include "math_extra.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_cone.cpp b/src/region_cone.cpp index 400fb072298d2d50b6b8cd1597a366f0b9c497f2..d669008e93e5f27b1fcdf384afb5567f4020e8bb 100644 --- a/src/region_cone.cpp +++ b/src/region_cone.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include "region_cone.h" -#include -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index dc1584a96bc6e371a741b2e553db9a6768a4d636..f7676a3d7475781c8e9fb54c727f000d042d2b03 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -12,14 +12,15 @@ ------------------------------------------------------------------------- */ #include "region_cylinder.h" -#include -#include -#include "update.h" + #include "domain.h" +#include "error.h" #include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_deprecated.cpp b/src/region_deprecated.cpp index afbe9e4189c880edc48c07e4abb8f6ccae3d4307..137c167ab9a76832255307d6ccdefada3d663b3e 100644 --- a/src/region_deprecated.cpp +++ b/src/region_deprecated.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "region_deprecated.h" -#include + #include "comm.h" #include "error.h" -#include "utils.h" + using namespace LAMMPS_NS; diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp index 4096657d3021026846400a2679f848475cf299d1..a61e2556b04480612b6b6045a7cfbbb044dcbc21 100644 --- a/src/region_intersect.cpp +++ b/src/region_intersect.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "region_intersect.h" -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_plane.cpp b/src/region_plane.cpp index bf12f3cd916acee2f0c1c22cd92d0f5439d64fdd..4895c1f081f5e0d26fcbc833eec0c90fb478c484 100644 --- a/src/region_plane.cpp +++ b/src/region_plane.cpp @@ -12,9 +12,10 @@ ------------------------------------------------------------------------- */ #include "region_plane.h" -#include + #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_prism.cpp b/src/region_prism.cpp index 5d7c5bce1fb6a6acc7c4aeffa1f623f9c22b3414..af270cc47f88067304d939374d4947c11e9e7588 100644 --- a/src/region_prism.cpp +++ b/src/region_prism.cpp @@ -16,11 +16,12 @@ ------------------------------------------------------------------------- */ #include "region_prism.h" -#include + #include "domain.h" -#include "force.h" -#include "math_extra.h" #include "error.h" +#include "math_extra.h" + +#include using namespace LAMMPS_NS; diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 44db951fded0da1f8c831bb3626a845e141362fc..4256af421381f7e557fc7642dce00430214a4a8f 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -12,13 +12,14 @@ ------------------------------------------------------------------------- */ #include "region_sphere.h" -#include -#include -#include "update.h" + +#include "error.h" #include "input.h" +#include "update.h" #include "variable.h" -#include "error.h" -#include "force.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/region_union.cpp b/src/region_union.cpp index 30f563df2ca855314e3f60305ee698e86d67a63f..677f1022f92d3fb2e14450c9746864d473955558 100644 --- a/src/region_union.cpp +++ b/src/region_union.cpp @@ -12,10 +12,11 @@ ------------------------------------------------------------------------- */ #include "region_union.h" -#include + #include "domain.h" #include "error.h" -#include "force.h" + +#include using namespace LAMMPS_NS; diff --git a/src/replicate.cpp b/src/replicate.cpp index 9c915d08c019abe387ffb46e4e19a532d73fcb0a..374d7113b29490e3b9ebf2895d7b37cddc885b24 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -12,19 +12,17 @@ ------------------------------------------------------------------------- */ #include "replicate.h" -#include -#include + +#include "accelerator_kokkos.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "domain.h" #include "comm.h" -#include "special.h" -#include "accelerator_kokkos.h" -#include "memory.h" +#include "domain.h" #include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "memory.h" +#include "special.h" + +#include using namespace LAMMPS_NS; diff --git a/src/rerun.cpp b/src/rerun.cpp index a63fd1ea55af86aed8cac012c52c677011425fea..51c0f6fdb25ac352602e8ad364972d17c59abe52 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "rerun.h" -#include -#include "read_dump.h" + #include "domain.h" -#include "update.h" +#include "error.h" +#include "finish.h" #include "integrate.h" #include "modify.h" #include "output.h" -#include "finish.h" +#include "read_dump.h" #include "timer.h" -#include "error.h" -#include "force.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp index 526de60cbab789a34ea07a8bc3ec4789e8968076..0b7cf9879f82ceca5867ef619905c5d7d668dfa2 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atom_ids.cpp @@ -12,19 +12,19 @@ ------------------------------------------------------------------------- */ #include "reset_atom_ids.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "domain.h" #include "comm.h" -#include "modify.h" +#include "domain.h" +#include "error.h" #include "fix.h" -#include "special.h" #include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "special.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index a6cfb69185897aaabc0d270f8eb5a37e71158a37..ad2caad6568230854227ea0755d015702ea0c24b 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -16,17 +16,17 @@ ------------------------------------------------------------------------- */ #include "reset_mol_ids.h" -#include + #include "atom.h" -#include "domain.h" #include "comm.h" -#include "group.h" -#include "modify.h" -#include "compute_fragment_atom.h" #include "compute_chunk_atom.h" -#include "utils.h" +#include "compute_fragment_atom.h" +#include "domain.h" #include "error.h" -#include "fmt/format.h" +#include "group.h" +#include "modify.h" + +#include using namespace LAMMPS_NS; diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index 9d2dd24bc8c176945f960a3911df295bb435c77c..fbb6fceb03bc32dcc2649ab068fec015e234df43 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -21,7 +21,6 @@ CommandStyle(reset_mol_ids,ResetMolIDs) #define LMP_RESET_MOL_IDS_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/respa.cpp b/src/respa.cpp index 1dcc4b898af60d7c7a9f4f9fdf199dedaef40e4a..c970c63a19e8fd3d8a0124fa7fc565b3d89abfd1 100644 --- a/src/respa.cpp +++ b/src/respa.cpp @@ -16,30 +16,29 @@ ------------------------------------------------------------------------- */ #include "respa.h" -#include -#include -#include "neighbor.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "domain.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "fix.h" +#include "fix_respa.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" -#include "fix_respa.h" -#include "timer.h" -#include "error.h" -#include "utils.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" #include "pair_hybrid.h" -#include "fmt/format.h" +#include "timer.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/run.cpp b/src/run.cpp index 91e2db5c6b8fbb1e49b92f09d798616c8dced5b7..166955d6acca198ac1593046e846f8374713de1c 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -12,17 +12,18 @@ ------------------------------------------------------------------------- */ #include "run.h" -#include + #include "domain.h" -#include "update.h" -#include "force.h" +#include "error.h" +#include "finish.h" +#include "input.h" #include "integrate.h" #include "modify.h" #include "output.h" -#include "finish.h" -#include "input.h" #include "timer.h" -#include "error.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/set.cpp b/src/set.cpp index b4a82e5c72f7365292dc389469c7eb92ea2a973e..3b2cd44ad08b4c760bf6a82140d8040046f5a86f 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -12,32 +12,30 @@ ------------------------------------------------------------------------- */ #include "set.h" -#include -#include -#include -#include + #include "atom.h" #include "atom_vec.h" +#include "atom_vec_body.h" #include "atom_vec_ellipsoid.h" #include "atom_vec_line.h" #include "atom_vec_tri.h" -#include "atom_vec_body.h" -#include "domain.h" -#include "region.h" -#include "group.h" #include "comm.h" +#include "domain.h" +#include "error.h" #include "force.h" +#include "group.h" #include "input.h" -#include "variable.h" -#include "random_park.h" -#include "random_mars.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" #include "memory.h" -#include "error.h" #include "modify.h" -#include "utils.h" -#include "fmt/format.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/special.cpp b/src/special.cpp index 3780fab5c0887e515af1312acde7a10883fa28da..eb74f534f7d679434507b35e12d39f97264b8df7 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -12,18 +12,16 @@ ------------------------------------------------------------------------- */ #include "special.h" -#include + +#include "accelerator_kokkos.h" // IWYU pragma: export #include "atom.h" +#include "atom_masks.h" #include "atom_vec.h" -#include "force.h" #include "comm.h" -#include "modify.h" #include "fix.h" -#include "accelerator_kokkos.h" // IWYU pragma: export -#include "atom_masks.h" +#include "force.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" using namespace LAMMPS_NS; diff --git a/src/table_file_reader.cpp b/src/table_file_reader.cpp index 525db2496132ab590cdd98f87010b3cf31e4ee24..50843c119eef96b68744218c1a76ec118f417db8 100644 --- a/src/table_file_reader.cpp +++ b/src/table_file_reader.cpp @@ -15,14 +15,10 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "error.h" #include "table_file_reader.h" -#include "utils.h" -#include "tokenizer.h" -#include "fmt/format.h" -#include +#include "text_file_reader.h" +#include "tokenizer.h" using namespace LAMMPS_NS; diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index 1e1e5e2ec19f8f8cf17908831f42916e6214b51b..3c63bba5fb0da358923a664d57e276ad7b2aa67c 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -15,14 +15,11 @@ Contributing authors: Richard Berger (Temple U) ------------------------------------------------------------------------- */ -#include "lammps.h" -#include "force.h" -#include "error.h" -#include "comm.h" -#include "utils.h" #include "text_file_reader.h" -#include "tokenizer.h" + #include "fmt/format.h" +#include "tokenizer.h" +#include "utils.h" #include diff --git a/src/text_file_reader.h b/src/text_file_reader.h index b64407701f8ae02c692d0b0c5093acdb0e75649c..65af0a08d9b4ac86c58fd058ff5ee4596b8929a8 100644 --- a/src/text_file_reader.h +++ b/src/text_file_reader.h @@ -18,11 +18,10 @@ #ifndef LMP_TEXT_FILE_READER_H #define LMP_TEXT_FILE_READER_H -#include -#include -#include #include "tokenizer.h" +#include + namespace LAMMPS_NS { class TextFileReader { diff --git a/src/thermo.cpp b/src/thermo.cpp index 96de72b4ab26248f1dc634b07ee105ac25b79a02..787b0cdda843961025a62a932d3b00e46b3286e0 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -16,37 +16,36 @@ // before lmptype.h can set flags to insure it is done correctly #include "thermo.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" -#include "update.h" +#include "bond.h" #include "comm.h" +#include "compute.h" +#include "dihedral.h" #include "domain.h" -#include "universe.h" -#include "lattice.h" -#include "group.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "neighbor.h" #include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" -#include "dihedral.h" +#include "group.h" #include "improper.h" +#include "input.h" #include "kspace.h" +#include "lattice.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "timer.h" -#include "memory.h" -#include "error.h" -#include "math_const.h" -#include "utils.h" -#include "fmt/format.h" #include "tokenizer.h" +#include "universe.h" +#include "update.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/timer.cpp b/src/timer.cpp index b9124978a9a2275f950c7f1188a98f7c43c828ca..adf143b4ae38d5d9fbdc4d150ae74667a2833d8f 100644 --- a/src/timer.cpp +++ b/src/timer.cpp @@ -12,13 +12,11 @@ ------------------------------------------------------------------------- */ #include "timer.h" -#include -#include -#include + #include "comm.h" #include "error.h" -#include "force.h" -#include "utils.h" + +#include #ifdef _WIN32 #include diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index eadff698cbbe86df8c8b1c89e50b1bca3ee3be8e..3b172181a2073c607cf07a3293d7c7f6b9f95d35 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -17,9 +17,11 @@ #include "tokenizer.h" #include "utils.h" -#include #include "fmt/format.h" +#include +#include + using namespace LAMMPS_NS; TokenizerException::TokenizerException(const std::string & msg, const std::string & token){ diff --git a/src/tokenizer.h b/src/tokenizer.h index eb19c4421b7c180ca9a050e5dcf564868b9b6e18..2db9870866e091389d09c9d51fe504fe45a43cd1 100644 --- a/src/tokenizer.h +++ b/src/tokenizer.h @@ -18,10 +18,11 @@ #ifndef LMP_TOKENIZER_H #define LMP_TOKENIZER_H -#include -#include #include "lmptype.h" -#include + +#include // IWYU pragma: export +#include // IWYU pragma: export +#include // IWYU pragma: export namespace LAMMPS_NS { diff --git a/src/universe.cpp b/src/universe.cpp index 45efb936e3f2b9e4e2f04d5575d39a2a95a8ca43..cd079a45c099b442a906a9f9fd81fe39a4a311bd 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -12,16 +12,13 @@ ------------------------------------------------------------------------- */ #include "universe.h" -#include -#include -#include -#include -#include "version.h" + #include "error.h" -#include "force.h" #include "memory.h" -#include "utils.h" -#include "fmt/format.h" +#include "version.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/update.cpp b/src/update.cpp index a1c712c35474add7c39bfbed2af08e451d576051..399584473c980e65f875199a12ebfa97b011184d 100644 --- a/src/update.cpp +++ b/src/update.cpp @@ -15,8 +15,8 @@ #include #include "integrate.h" #include "min.h" -#include "style_integrate.h" -#include "style_minimize.h" +#include "style_integrate.h" // IWYU pragma: keep +#include "style_minimize.h" // IWYU pragma: keep #include "neighbor.h" #include "force.h" #include "modify.h" @@ -61,7 +61,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) #define INTEGRATE_CLASS #define IntegrateStyle(key,Class) \ (*integrate_map)[#key] = &integrate_creator; -#include "style_integrate.h" +#include "style_integrate.h" // IWYU pragma: keep #undef IntegrateStyle #undef INTEGRATE_CLASS @@ -70,7 +70,7 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp) #define MINIMIZE_CLASS #define MinimizeStyle(key,Class) \ (*minimize_map)[#key] = &minimize_creator; -#include "style_minimize.h" +#include "style_minimize.h" // IWYU pragma: keep #undef MinimizeStyle #undef MINIMIZE_CLASS diff --git a/src/update.h b/src/update.h index e70325a4984b3e62f6df0bfa247b364533136a7b..558719f4ccadaadf7a64d893dd3787bd56a70fd0 100644 --- a/src/update.h +++ b/src/update.h @@ -15,8 +15,8 @@ #define LMP_UPDATE_H #include "pointers.h" + #include -#include namespace LAMMPS_NS { diff --git a/src/utils.cpp b/src/utils.cpp index 9d60ad01b604c7d67c0660569a24a9da43352d70..af800f48b067ecfd8b8bc51892975b2b6d61d939 100644 --- a/src/utils.cpp +++ b/src/utils.cpp @@ -12,20 +12,20 @@ ------------------------------------------------------------------------- */ #include "utils.h" -#include -#include -#include -#include "lammps.h" + #include "comm.h" #include "compute.h" #include "error.h" #include "fix.h" #include "memory.h" #include "modify.h" -#include "tokenizer.h" #include "text_file_reader.h" +#include "tokenizer.h" #include "update.h" -#include "fmt/format.h" + +#include +#include +#include #if defined(__linux__) #include // for readlink diff --git a/src/variable.cpp b/src/variable.cpp index d16987984f5264f6aef3a0805d1e241e3c413377..8d4416dfa71d98631e9b827505068fe7e8a5731a 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -12,36 +12,33 @@ ------------------------------------------------------------------------- */ #include "variable.h" -#include -#include -#include -#include -#include -#include -#include -#include "universe.h" + #include "atom.h" -#include "update.h" -#include "group.h" -#include "domain.h" #include "comm.h" -#include "region.h" -#include "modify.h" #include "compute.h" -#include "input.h" +#include "domain.h" +#include "error.h" #include "fix.h" #include "fix_store.h" -#include "force.h" -#include "output.h" -#include "thermo.h" -#include "random_mars.h" -#include "math_const.h" +#include "group.h" +#include "info.h" +#include "input.h" #include "lmppython.h" +#include "math_const.h" #include "memory.h" -#include "info.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "modify.h" +#include "output.h" +#include "random_mars.h" +#include "region.h" +#include "thermo.h" +#include "universe.h" +#include "update.h" + +#include +#include +#include +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/variable.h b/src/variable.h index f5ea11c0b4ba22de847e05fcd44ef2f21ac34fc4..efffacc7bba4cf2a7132ef7e8ca2f8319e0ecd32 100644 --- a/src/variable.h +++ b/src/variable.h @@ -15,7 +15,6 @@ #define LMP_VARIABLE_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/velocity.cpp b/src/velocity.cpp index 140a3969261c167495780e8e61670dd230231f63..eafa98cb7cbfa7c17d8b03bf9f8db6c46bfb0944 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -12,24 +12,24 @@ ------------------------------------------------------------------------- */ #include "velocity.h" -#include -#include + #include "atom.h" -#include "domain.h" -#include "lattice.h" -#include "input.h" -#include "variable.h" -#include "force.h" -#include "modify.h" -#include "fix.h" +#include "comm.h" #include "compute.h" #include "compute_temp.h" -#include "random_park.h" +#include "domain.h" +#include "error.h" +#include "fix.h" #include "group.h" -#include "comm.h" +#include "input.h" +#include "lattice.h" #include "memory.h" -#include "error.h" -#include "utils.h" +#include "modify.h" +#include "random_park.h" +#include "variable.h" + +#include +#include using namespace LAMMPS_NS; diff --git a/src/verlet.cpp b/src/verlet.cpp index 97c5f918b5f8a5dd66a6df6d1cfbfa4d49c0f7b3..a7b9ba4c225bab923ac7c472516031c11dbaa408 100644 --- a/src/verlet.cpp +++ b/src/verlet.cpp @@ -12,26 +12,26 @@ ------------------------------------------------------------------------- */ #include "verlet.h" -#include -#include -#include "neighbor.h" -#include "domain.h" -#include "comm.h" + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "force.h" #include "improper.h" #include "kspace.h" -#include "output.h" -#include "update.h" #include "modify.h" +#include "neighbor.h" +#include "output.h" +#include "pair.h" #include "timer.h" -#include "error.h" -#include "fmt/format.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 612f5bb123e54ac3d00d81d94b89b52121152615..121a2ed1fda68f95a05d4da70347811a6f247330 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -12,22 +12,21 @@ ------------------------------------------------------------------------- */ #include "write_coeff.h" -#include -#include -#include -#include -#include "pair.h" -#include "bond.h" + #include "angle.h" -#include "dihedral.h" -#include "improper.h" +#include "bond.h" #include "comm.h" +#include "dihedral.h" +#include "domain.h" +#include "error.h" #include "force.h" +#include "improper.h" +#include "pair.h" #include "universe.h" -#include "error.h" -#include "domain.h" -#include "utils.h" -#include "fmt/format.h" + +#include +#include +#include using namespace LAMMPS_NS; diff --git a/src/write_data.cpp b/src/write_data.cpp index d549d8bf774386acdfaa072dde12aa7dc6ab72ad..53d277b72367d98e56b2bb7d745558d8b700347e 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -12,29 +12,27 @@ ------------------------------------------------------------------------- */ #include "write_data.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" #include "improper.h" -#include "update.h" +#include "memory.h" #include "modify.h" -#include "fix.h" -#include "domain.h" -#include "universe.h" -#include "comm.h" #include "output.h" +#include "pair.h" #include "thermo.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" + +#include using namespace LAMMPS_NS; diff --git a/src/write_data.h b/src/write_data.h index e94e7f559532a2203af70176da7a1e7ed98bc698..a4e71c9cda2f1ce6c2ee5e88ec96ec241dda7225 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -21,7 +21,6 @@ CommandStyle(write_data,WriteData) #define LMP_WRITE_DATA_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/src/write_dump.cpp b/src/write_dump.cpp index 9b257b9ab06e9f0d7bd0b5a0485ab9baac3e0aba..56839a2f5e47ffcd96b55d05e5f669aa8f956219 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -16,15 +16,16 @@ ------------------------------------------------------------------------- */ #include "write_dump.h" -#include -#include #include "style_dump.h" + +#include "comm.h" #include "dump.h" #include "dump_image.h" -#include "comm.h" -#include "update.h" #include "error.h" -#include "utils.h" +#include "update.h" + +#include + using namespace LAMMPS_NS; diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 22e993c37c86273a3df16407dcf014de3b249d34..256d7a377ee5b1c7668501efb39bc682bcd301c6 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -12,32 +12,30 @@ ------------------------------------------------------------------------- */ #include "write_restart.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "group.h" -#include "force.h" -#include "pair.h" #include "bond.h" -#include "angle.h" +#include "comm.h" #include "dihedral.h" -#include "improper.h" -#include "update.h" -#include "neighbor.h" #include "domain.h" -#include "modify.h" +#include "error.h" #include "fix.h" -#include "universe.h" -#include "comm.h" +#include "force.h" +#include "group.h" +#include "improper.h" +#include "memory.h" +#include "modify.h" +#include "mpiio.h" +#include "neighbor.h" #include "output.h" +#include "pair.h" #include "thermo.h" -#include "mpiio.h" -#include "memory.h" -#include "error.h" -#include "utils.h" -#include "fmt/format.h" +#include "universe.h" +#include "update.h" + +#include #include "lmprestart.h" diff --git a/src/write_restart.h b/src/write_restart.h index 5056f50636b23bc33b58b27ef76df0300897ecde..a4a606482e37dc1d35c83a7ae1195f0b4a9e2baf 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -21,7 +21,6 @@ CommandStyle(write_restart,WriteRestart) #define LMP_WRITE_RESTART_H #include "pointers.h" -#include namespace LAMMPS_NS { diff --git a/tools/msi2lmp/src/WriteDataFile.c b/tools/msi2lmp/src/WriteDataFile.c index c03eba71c5f2b52f7e54b53c45bb8e9b2cdd985a..a6f1615809ac2c2988a30d9740854850512ef928 100644 --- a/tools/msi2lmp/src/WriteDataFile.c +++ b/tools/msi2lmp/src/WriteDataFile.c @@ -3,7 +3,6 @@ */ #include "msi2lmp.h" -#include "Forcefield.h" #include diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index efc929639a937da885526107e02d3aa2484093ae..b5e9a96293464bb192cd21e98b52c7af3df1af56 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -151,7 +151,6 @@ #include #include -#include /* global variables */ diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index c9b198444443950699af5851adccce89ec8e4338..af7978d181d6ce5743b40f88dcda9e0c2a5dbc90 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -34,7 +34,7 @@ * compatibility with the obsolete LAMMPS version written in Fortran 90. */ -# include +#include /* IWYU pragma: export */ #define MSI2LMP_VERSION "v3.9.9 / 05 Nov 2018" diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index a409f3547c015ba034e4bcc336ce0debac2268b6..80ee3926c85dab7869d6e7756e4df5985af8e209 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -28,6 +28,7 @@ #include #include #include +#include #include #if !defined(_FORTIFY_SOURCE) || (_FORTIFY_SOURCE == 0) diff --git a/unittest/formats/test_pair_unit_convert.cpp b/unittest/formats/test_pair_unit_convert.cpp index 6c4b38397d83252d4f4e813dc5ebbac855a31373..8571c7b4423086c5cc142ea3faa24168d8676637 100644 --- a/unittest/formats/test_pair_unit_convert.cpp +++ b/unittest/formats/test_pair_unit_convert.cpp @@ -15,17 +15,15 @@ #include "force.h" #include "info.h" #include "input.h" -#include "lammps.h" #include "output.h" #include "pair.h" #include "thermo.h" -#include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" -#include +#include #include -#include +#include // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp index f5b298874f00b1a1c4890add7beb4288237fbaef..aaa52b11423d4847e975295e536005b5d271058f 100644 --- a/unittest/formats/test_potential_file_reader.cpp +++ b/unittest/formats/test_potential_file_reader.cpp @@ -13,7 +13,6 @@ #include "MANYBODY/pair_comb.h" #include "MANYBODY/pair_comb3.h" -#include "MANYBODY/pair_eim.h" #include "MANYBODY/pair_gw.h" #include "MANYBODY/pair_gw_zbl.h" #include "MANYBODY/pair_nb3b_harmonic.h" @@ -26,13 +25,13 @@ #include "USER-MISC/pair_tersoff_table.h" #include "info.h" #include "input.h" -#include "lammps.h" #include "potential_file_reader.h" -#include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include +#include +#include #include #if defined(OMPI_MAJOR_VERSION) diff --git a/unittest/utils/test_fmtlib.cpp b/unittest/utils/test_fmtlib.cpp index fd9a4a06a2240261e1b5e1bc459edd4833eb4118..7233d0ab1a615e8464358ae3842d7582994b8e50 100644 --- a/unittest/utils/test_fmtlib.cpp +++ b/unittest/utils/test_fmtlib.cpp @@ -16,7 +16,6 @@ #include "gmock/gmock.h" #include "gtest/gtest.h" #include -#include using namespace LAMMPS_NS; using ::testing::Eq; diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp index 7cef3cead0aa07c4726d3442ea03e60ae4cd622f..28656ef9c8c6071e65743c9f90d95d1f5558a486 100644 --- a/unittest/utils/test_tokenizer.cpp +++ b/unittest/utils/test_tokenizer.cpp @@ -11,6 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" #include "tokenizer.h" #include "gmock/gmock.h" #include "gtest/gtest.h" diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp index 69076fcbd9e807d53a81ff8f963e5577bd31da5a..9a2c5eb4df000b3fada75686a16ec7a0d96b9c86 100644 --- a/unittest/utils/test_utils.cpp +++ b/unittest/utils/test_utils.cpp @@ -11,12 +11,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +#include "lmptype.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include #include -#include #include #include